A proposal for the AIMS Bioresources Library to be declared a Wildlife Trade
Operation (WTO) under the Environment Protection and Biodiversity Conservation
Act 1999 (EPBC Act), so that samples can be exported to facilitate biodiscovery
Research and Development.
Libby Evans-Illidge, Manager, Bioresources Library
Australian Institute of Marine Science
Contact: email bioresources@aims.gov.au
Submitted 8th April 2009; amended 16 August 2011
1. Introduction:
The Australian Institute of Marine Science (AIMS) is a Commonwealth Statutory
Authority established by the Australian Institute of Marine Science Act of 1972, to
provide the research capacity to facilitate the management and sustainable development
of Australia’s marine environment and resources. The institute’s biodiscovery research
aims to access and document Australia’s marine biodiversity and to discover molecules
(eg chemicals, genes) which may be developed by industrial partners into clinically useful
drugs or other beneficial products. Collaborations with industrial partners and other
research institutions have been instrumental in the development and success of this
initiative over the past 20 years. Since a review undertaken in 2005, AIMS has refocused
its core efforts on the curation of the AIMS Bioresources Library, and facilitating access
to it for biodiscovery effort.
Biodiscovery R&D involves systematically searching through the molecular diversity
present in nature, for currently unknown molecules that are capable of producing a
desired reaction in a molecular process associated with some commercial application.
Laboratory tests called bioassays or screens are designed to mimic the target molecular
system and allow detection of the desired reaction. The odds of discovering a new
commercial product through biodiscovery are long. Target product areas in which AIMS
has had previous research interest include pharmaceuticals, agrichemicals, industrial
enzymes, sunscreens, toxin testing kits, antifoulants, bioremediation, environmental
monitoring. However, the benefits of biodiscovery go beyond commercial outcomes, and
include many non-commercial benefits such as documentation of biodiversity and an
understanding of the chemical ecology of marine systems, as a foundation for their better
management of resources. Besides facilitating pathways to commercialization of its
biodiscovery research, AIMS seeks to also maximise the non-commercial outcomes,
particularly those that contribute to capacity building within Australia, and the
conservation and sustainable management of marine resources.
The cornerstone of AIMS’ biodiscovery effort is the AIMS Bioresources Library. This is
a library of samples which is representative of Australia’s marine biodiversity and curated
specifically for biodiscovery research. The Bioresources Library is considered to be the
most comprehensive assemblage of Australian marine organisms for this purpose in the
world. Additions to the Bioresources Library are ongoing. To date, over 10 000 marine
macroorganisms and 8000 marine microorganisms have been collected from about 1600
different sites around Australia. The collection exhibits a high proportion of new and/or
endemic species, and represents all major marine phyla from diverse habitats. While
microorganisms are currently outside the scope of the export provisions of the EPBC Act,
they are included in this application to cover their potential integration into the export
regulations in the future. Table 1 includes a list of phyla included in the collection.
Table 1: List of phyla included in the AIMS Bioresources Library:
Phylum
Plants:
Angiospermata
Chlorophyta
Cyanophyta
Phaeophyta
Rhodophyta
Animals:
Annellida
Brachiopoda
Bryozoa
Chordata
Cnidaria
Crustacea
Echinodermata
Echiura
Hemichordata
Mollusca
Nemertina
Phoronida
Platyhelminthes
Porifera
Protista
Sipuncula
Microorganisms:
Actinomycetes
Fungi
Archaeobacteria
Eubacteria
Cyanobacteria
Common Names
Flowering plants (seagrass, mangroves)
Green algae
Blue-green algae
Brown algae
Red algae
Segmented worms
Lamp shells
Lace coral
Fish, tunicates
Corals, hydroids, jelly fish
Crabs,lobsters,shrimp etc
Starfish, urchins, sea cucumbers
Spoon worms
Acorn worms
Shell fish, nudibranchs
Ribbon worms
Horseshoe worms
Flat worms
Sponges
Forams
Peanut worms
2
The collection contains a high proportion of new species, and samples from poorly
described groups. Hence it is often initially only possible to categorise samples according
to higher order taxonomy. The AIMS collection is taxonomically biodiverse, and includes
all major marine phyla as listed in table 1. One of the benefits of further research and
development with the collection is more detailed taxonomy and description of new
species. To facilitate this, AIMS has close linkages to Australia’s museums to maximize
the synergy between biodiscovery and biosystematics, and in may accept frozen duplicate
material from their reference collections into the Bioresources Library, so that it can be
made available for biodiscovery research effort through AIMS.
In some cases, samples collected do include species regulated under Appendix II to the
Convention on International Trade in Endangered Species of Fauna and Flora (CITES).
(eg common species of hard corals and tridacnid clams). Specimens of any species listed
under Appendix I to CITES cannot be exported under a WTO and do not form part of this
proposal. In addition, specimens of species listed as threatened (excluding the
conservation dependent category) under Section 178 of the EPBC Act will not be
collected or exported under this proposal.
While Australia boasts significant scientific infrastructure for biodiscovery research based
at a range of research organisations including AIMS, there are currently many potential
international opportunities in this field which are not available within Australia. The
range of target product areas is limited within Australia compared to that available
globally. Also, large international companies provide major research funding
opportunities that are currently unable to be drawn from Australian industry. These can be
opportunities for investment in the further capability of Australian organizations.
Clearly, access to strategic overseas collaborations which maximise Australian
participation in research and development and subsequent commercialisation of product
leads is fundamental to maximising the potential of biodiscovery research within
Australia. However, replication of all overseas capability within Australia is neither
reasonable nor viable, and the more effective model is to seek complimentary capability
with overseas collaborators. Thus, movement of sample material overseas, under strict
material transfer and license terms of binding agreements, is necessary.
In 2004, AIMS obtained WTO status for its holdings under the EPBC Act, but this has
now expired. This proposal supports an application to renew that WTO status, to facilitate
biodiscovery effort using the AIMS Bioresources Library, into the future.
Bioresources from WA state waters are outside the scope of this WTO proposal:
AIMS, along with the Western Australian Museum, became founding partners of the
Western Australian Marine Science Institute (WAMSI) in 2007. Their activities within
WAMSI included establishing the Western Australian Marine Bioresources Library
(WAMBL), as the primary biodiscovery repository for WA marine fauna, and AIMS
consented to all AIMS Bioresources Library material sourced from WA State waters, to
be incorporated into WAMBL. As such, access to these samples for biodiscovery use
3
now requires the authority of the WA Museum through WAMBL procedures, which rely
on the (WA) Fish Resources Management Regulations 1995 (FRMR) Regulation 179 to
handle samples for biodiscovery curation and use, regardless of the permit which
authorised the original collection of samples.
In the original version of this proposal, the intention was for the WA State samples to
remain within the scope of the AIMS WTO, in order to facilitate their transfer to
international parties where access had been authorised by WAMBL and the WA
Department of Fisheries (ie authority granted under WA Fish Resources Management
Regulations). However, the WA Department of Environment and Conservation (DEC),
have raised concerns about the inclusion of samples within the scope of this WTO that
were collected under their legislation (including predecessors) which are conditioned to
preclude commercial and/or biodiscovery use. Due to the need to resolve policy issues
surrounding the granting of a FRMR Regulation 179 authority to handle samples
collected under the authority of another WA State agency, and in the interests of
avoiding further time delays which would prevent the remainder of the AIMS
Bioresources library from WTO status and therefore access to international transfers, all
samples collected under the authority of DEC, or their predecessor (Department of
Conservation and Land Management, CALM) have been removed from the scope of this
proposal. WAMBL or AIMS may submit a separate WTO application to cover them, in
due course and after issues are resolved.
2. The Proposal Objectives:
This is a proposal for the AIMS Bioresources Library to be declared a Wildlife Trade
Operation, so that samples (chemical extracts, pure compounds, DNA preparations, etc)
derived from the Bioresources Library may be exported to international collaborators in
biodiscovery research. The objectives sought are:



Legal certainty over the terms and conditions of AIMS ability to export samples to
collaborators, in order to be able to attract collaborative opportunities;
Declaration of the AIMS Bioresources Library as a WTO, with provision for
regular updating of the inventory to account for new acquisitions. This will allow
samples from AIMS Bioresources Library to be included in collaborations in the
future (subject to legally binding agreements and the terms of access and benefit
sharing agreements);
Transparent and clear administrative process for each export.
The purpose of these activities is to maximise the potential for discovering commercial
products and other new knowledge from Australia’s marine biodiversity, for the benefit
of Australia. This will be achieved by accessing resources and capability which are
currently unavailable to AIMS within Australia, in a way that captures opportunities for
capacity building and intellectual property development within Australia and provides for
equitable benefit sharing.
4
3. Harvest Details
3.1 Harvest areas, and ownership.
Collection sites were selected to span as great a range of geographic and ecological
gradients as possible (see Figure 1). Access to Australia’s marine environment for the
purposes of undertaking collections for biodiscovery research is controlled by a complex
array of legislation administered at all levels of government, and samples in the AIMS
Bioresources Library have been derived from almost all marine jurisdictions in
Australia’s ocean territory. (note, that those collected with the authority of the WA
Department of Environment and Conservation and its predecessor are excluded from
figure 1 and the scope of this WTO application). Where appropriate, as determined by
site location, taxonomic groups collected, and equipment used, collection permits have
been obtained. Attachment 1 summarises permits obtained to date for samples included in
this WTO proposal (Note that collections date back to 1987, and in some cases
departments have been renamed and legislation replaced since that time).
All sites are marine, and to date, there has been no non-crown ownership of collection
sites. However, AIMS has is aware of the potential for future recognition of traditional
ownership over some marine areas, and intends to proactively engage with traditional
owners as appropriate.
Figure 1: Map of Australia showing collection locations for material included in
this WTO proposal.
5
3.2 Harvest methods and quantities.
All AIMS collection activities are controlled by established AIMS collection protocols
(see Attachment 2). All personnel that participate in collection activities are trained in the
application of these protocols, and most are trained marine scientists. These protocols
ensure that rare organisms are not taken and populations of common species are not
unsustainably depleted. By nature, collecting for biodiscovery involves the collection of a
small quantity of a large range of organisms. Collection methods employed by AIMS
include hand picking by intertidal or SCUBA diving activities in depths of less than 20
metres, and deployed sampling equipment such as trawl, grab and dredge gear for deeper
‘undivable’ sites. The targeted quantity for primary collection is 10-500g (wet organism
weight) plus a representative taxonomic voucher per sample.
The majority of sites visited to date have been accessible to hand picking methods. This
style allows selective collections and negligible incidental damage. Collection procedures
ensure minimal environmental impact by favouring sub-sampling of individuals where
possible. For example, thin encrusting organisms are sampled from one ‘front’ only and
at least one third of each individual is left intact. In the case of large solitary sessile
modular organisms, at least one third of each organism including the holdfast area is left
intact. AIMS research has shown that collection of modular organisms in this way can
avoid mortality. If the organism is not modular and sub-sampling is not possible, the
minimum number of individuals required to achieve between 10 – 200g (wet weight) plus
a taxonomic voucher is collected. Often, this requires the collection of only two
individuals. The requirement to locate at least two individuals on a single dive ensures
that rare organisms are avoided.
In recognising that most of Australia’s Ocean Territory is inaccessible to diving, AIMS
has begun to access deeper areas using appropriate equipment. While the necessary
deployed deep sampling gear is less selective and in comparison to hand picking more
incidentally destructive, impacts are minimised through restricted size of the equipment.
For example, the otter trawl gear has a single 3 fathom collecting net, less than half the
size of one of the multiple nets used in commercial fishing. Such modest equipment is
adequate for the small sample quantities required for biodiscovery collecting.
Where AIMS accessions frozen duplicate material from Museums into the Bioresources
Library, it ensures that similar collection protocols were employed.
AIMS sample processing procedures are tailor-made to enable subsequent systematic,
biological and ecological studies as well as natural product screening. In addition to
material for freezing and the production of chemical extracts for screening, an
appropriately preserved and taxonomically representative voucher is collected for each
sample. Extensive field data is recorded, including specimen and habitat descriptions and
imagery. This material and data is a significant resource for biodiversity documentation
and management, and AIMS collections have been utilised in the past for major
taxonomic revisions. The vouchers are initially housed and curated at AIMS but
6
ultimately lodged with an appropriate public institution. To date, over 6500 specimens
have been lodged at the Queensland Museum and are readily accessible to the research
community through their loans program.
Should the compound proceed to become a new commercial product, all options for long
term large scale supply of compound would be assessed on their merit. While ongoing
wild harvest of abundant and fecund species may technically be ecologically sustainable,
such an option would be least favourable and only considered if the organism was not
amenable to culture or the compound to synthesis. These latter two options represent
exciting opportunities for emerging new mariculture and chemical industries in this
country.
In addition to the protocol outlined above, which AIMS has proactively developed and
voluntarily applied, samples in the AIMS Bioresources Library have been collected
legally, and where required, under a permit from the relevant regulatory authorities (often
more than one for any sample). Attachment 1 lists the permits obtained to date. Thus,
collection activities have also been regulated by the conditions of these permits.
3.3 Harvest Timing
The AIMS Bioresources Library has been acquired over a sustained period since 1987,
from a wide range of jurisdictions (Attachment 1). Collection activities are ongoing, with
the ultimate aim of curating a collection which comprehensively represents Australia’s
marine biodiversity.
3.4 Non-AIMS collections
AIMS has recently implemented a policy of accessioning appropriately curated frozen
material from collections held by other insitutions, into the AIMS Bioresources Library.
This policy will ensure the maximum value is derived from available collection effort,
especially regarding publicly funded biodiversity surveys and assessments. Once
accessioned, samples would be treated as if AIMS had undertaken the collection, with
benefit sharing arrangements applying depending on the location of the collection (and
identification of the relevant jurisdiction and ‘resource provider’). However, such
accessions need to meet strict quality criteria prior to being considered for accession,
including:
o Full collection data is available, including precise collection location and dates
o The collection must be covered by appropriate permits, and full access must be
provided to relevant permits covering collection and subsequent use
o Collections must have been undertaken un a sustainable manner, with collection
protocols used at least to the standard of those practiced by AIMS (Attachment 2)
o Must be a taxonomic voucher available at a research organisation (doesn’t have to
be transferred to AIMS but must be maintained into the future).
o Full and prior informed consent for the accession into the AIMS Bioresources
Library, prior to the sample being used in biodiscovery screening.
7
No samples have been accessioned under this policy to date, however discussions are
underway with the Queensland Museum, Geosciences Australia, and the Northern
Territory Museum.
4. Impact of harvest on the taxa and the relevant ecosystem.
Despite the fact that primary collections are made from poorly understood groups of
organisms, the sampling protocols outlined above and in Attachment 2 and regulatory
conditions attached to collection permits ensure that collection activities cause no more
than minimal impact on the taxa and the relevant ecosystem. Generally, this is because
rare organisms are avoided, and only small amounts of each species is collected, often in
a way that does not cause mortality.
5. Monitoring and Assessment, management, and compliance.
As detailed above, while primary collection activities do not include formal assessment
and monitoring, the method of collection is designed to avoid local depletion of species.
To some extent, application of the collection protocols includes a degree of gross
assessment of abundance (eg in order to avoid rare species). Reports to regulatory
agencies provide a vehicle for audit of AIMS collection activities.
In addition to AIMS commitment for responsible action at all times, there is another
powerful incentive for compliance when it comes to biodiscovery. This is the requirement
for AIMS to provide funds providers (including industry) with an absolute warranty as to
the legal certainty over its right to provide access to the material for the R&D. Investors
are not interested in investing in the work if there is a chance of legal obstacles to
developing the outcomes.
6. Reports
AIMS will be pleased to continue reporting to the relevant department responsible for
application of the EPBC Act, on collection and export activities. After discussion with
officers of the Department of Sustainabiliyt Environment Water Population and
Communities, annual WTO reporting is proposed to be incorporated into the annual
reporting required of the AIMS-Commonwealth Benefit Sharing Deed. This report will
include information provided under the previous AIMS WTO, including an update of
samples in the AIMS Bioresources Library, and a list of international material transfers.
8
ATTACHMENT 1
Details of approvals and permits relating to the AIMS Bioresources Library
(AIMS Bioresources Library = AIMS Marine Biodiversity Collection referred to in WTO declaration 31-03-2005)
The purpose of exports from the AIMS WTO is to facilitate biodiscovery research with Australia’s marine biodiversity, that may lead to
commercialisation of outcomes (eg discovery of a new drug candidate from a marine organism). The samples have been sourced from over 1600
sites from all marine jurisdictions within Australia’s EEZ. The regulatory framework for using biodiversity in biodiscovery research is still
emerging in Australia, in line with the Convention on Biological Diversity (access and benefit sharing provisions) and Australia’s Nationally
Consistent Approach.
The following table lists permits and agreements obtained from relevant Australian authorities to date, for the collection and use of material in the
proposed AIMS WTO. Copies of actual documents can be provided on request.
NONAIMS_PARTY
Qld Fisheries
GBRMPA
GBRMPA
Dept of Transport and
Regional Services
LEGISLATION
Queensland
Fisheries Act 1994
GBRMPA
Regulation
GBRMPA
Regulation
THEIR_REFERENCE
_NUM
ISSUE_
DATE
START_
DATE
END_
DATE
EFFECTIVE
_END_DATE
JURISDICTION
QP053
20/03/1996
20/03/1996
31/12/1996
31/12/1996
QLD
G94/587
30/01/1995
14/02/1995
31/12/1996
18/09/2002
QLD
AIMS General Permit
G94/702
14/12/1994
15/12/1994
14/12/1995
14/12/1995
QLD
Genus Conus only. A/Prof Paul Alewood
Letter indicating that no permit required for
Coral Sea Island Territories if outside
National Nature Reserves
Nil
30/10/2002
13/11/2002
26/11/2002
26/11/2002
AUST
01NOCA2371
28/11/2001
28/11/2001
27/11/2004
27/11/2004
QLD
COMMENTS
QLD FISHERIES
Nil
QLD Fisheries Act
1994
QLD FISHERIES
QLD Fisheries Act
1994
01NOCA8064FR2371
19/07/2004
28/11/2001
27/11/2004
27/11/2004
QLD
Allows collection of Marine Plants
Modification to Permit 01NOCA2371
allowing collection of sponges in Torres
Straits
NSW Fisheries
Fisheries
Management Act
P03/0038
19/05/2003
19/05/2003
31/05/2004
31/05/2004
NSW
Recollection of sponges from Wollongong
area
NONAIMS_PARTY
LEGISLATION
1994
Australian National
Parks and Wildlife
Service
National Parks and
Wildlife
Regulations
GBRMPA
Regulation
GBRMPA
Dept of Fisheries
Dept of Fisheries
Fisheries Resources
Management Act
Fish Resources
Management Act
1994
Queensland Dept of
Primary Industries
THEIR_REFERENCE
_NUM
ISSUE_
DATE
ASH397
14/06/1996
01/06/1988
Ref: 256/02
12/10/1997
98 NOTO 0622
START_
DATE
END_
DATE
EFFECTIVE
_END_DATE
JURISDICTION
COMMENTS
31/12/1997
31/12/1997
AUST
Permit to collect in Ashmore Reef National
Nature Reserve
01/06/1988
15/02/1993
15/02/1993
QLD
Start date is date project moved to aims.
04/10/2002
31/12/2002
31/12/2002
WA
Authority to Handle Fish for Genetic or
Chemical Extraction or Analysis
WA
AIMS Exemption from 7(3) of fisheries Act
12/10/1997
03/09/1989
02/09/2001
02/09/2001
QLD
Institute-wide fisheries Resources Permit
NSW Department of
Agriculture
GBRMPA
Regulation
GBRMPA
Regulation
GBRMP
Regulations;
Marine Park
Regulation 1983
(Qld)
Qld Fisheries Act
1976-1984 (section
58)
Fisheries and
Oyster Farms Act
1935
Dept of Conservation
Forests and Lands
Fisheries Act
(1968)
89-R-38
14/11/1990
05/02/1990
19/02/1990
19/02/1990
VIC
Dept of Sea Fisheries
Tasmania
Fisheries Act 1959
Section 52
7/1/14/63
19/02/1990
19/02/1990
04/03/1990
04/03/1990
TAS
GBRMPA
GBRMPA
GBRMPA
Qld Department of
Primary Industaries
G87/109
13/04/1987
14/04/1987
13/04/1988
13/04/1988
QLD
Cairns and Far North Queensland Section
G87/293
09/10/1987
09/10/1987
22/10/1987
22/10/1987
QLD
Central Section
G88/171a & G88/171b
04/05/1988
05/05/1988
04/05/1989
04/05/1989
QLD
Central Section & Townsville/Whitsunday
Marine Park
1780
05/02/1987
05/02/1987
05/07/1992
05/07/1992
QLD
reefs in the vicinity of Townsville, Orpheus
Island and in the Torres Straits
29/01/1988
31/03/1988
31/03/1988
NSW
F87/1859 PJE;HB
10
THEIR_REFERENCE
_NUM
ISSUE_
DATE
START_
DATE
END_
DATE
7/1/14/63
15/01/1991
15/01/1991
28/02/1991
91/93
12/11/1990
01/02/1991
Fisheries Act 1982
Section 41
DF 16/31
12/01/1989
Aboriginal Lands
Council
Aboriginal Land
Act 1980
DHA/644-651 GAL/
134-141
Fisheries Dept
Fisheries Act 1905
Section 20
NONAIMS_PARTY
LEGISLATION
Dept of Sea Fisheries
Tasmania
Dept of Parks,
Wildlife and Heritage
Fisheries Act 1959
Section 52
National Parks and
Wildlife Act 1970
Section 35
SA Dept of Fisheries
GBRMPA
Fisheries Act 1905
Section 20
GBRMPA
Regulation
GBRMPA
GBRMPA
Regulation
Australian Fisheries
Management
Authority
Fisheries
Management Act
1991
Department of
Primary Industry
Queensland
Fisheries Act 1994
Fish Resources
Management Act
1994
Fisheries Dept
Dept of Fisheries
NA
NA
Fisheries Dept
GBRMPA
Fisheries Act 1905
Section 20
GBRMPA
JURISDICTION
COMMENTS
28/02/1991
TAS
Permit Reissued
28/02/1991
28/02/1991
TAS
Applies to Conservation reserves and
conservation areas
12/01/1989
31/03/1989
31/03/1989
SA
17/09/1990
10/11/1990
20/11/1990
20/11/1990
NT
FD 526/75 V4
06/09/1990
12/09/1990
19/09/1990
19/09/1990
WA
FD 526/75 ?V5
23/08/1991
01/08/1991
01/09/1991
01/09/1991
WA
G05/11866.1
02/05/2005
05/08/2005
31/08/2008
31/08/2008
QLD
Project collection permit
QLD
AIMS General permit. End data extended
while new permit application being
considered by GBRMPA.
G88/354
21/09/1988
21/09/1988
20/09/1989
EFFECTIVE
_END_DATE
14/02/1995
900156
14/11/1996
20/11/1996
19/12/1996
19/12/1996
NSW
Permit issued to CSIRO and covers water
off NSW and Victoria but AIMS samples
only collect off NSW coast.
96SODB0979
01/10/1996
01/10/1996
30/06/1997
30/06/1997
QLD
Oil spill experiment project (Michelle
Ramsey)
01/07/2001
01/07/2001
30/07/2003
30/07/2003
WA
Permit exempting AIMS from WA Fisheries
Act
TAS
No permit required, bycatch on fishing
license. Find correspondence re AFMA
observer and AIMS.
WA
QLD
AIMS General Research Permit
FD 526/75 V3
G02/4011.1
11/09/2002
01/03/1989
18/09/2002
31/03/1989
31/08/2005
31/03/1989
31/08/2005
11
NONAIMS_PARTY
GBRMPA
DPIF Fisheries
Division
Department of
Primary Industries
and Fisheries
(Tasmania)
LEGISLATION
Regulation
GBRMPA
Regulation
Northern Territory
of Australia
Fisheries Act
Fisheries Act 1959
THEIR_REFERENCE
_NUM
ISSUE_
DATE
START_
DATE
END_
DATE
G00/506
2003-2004/S17/1756
and 20032004/S17/1755
10/10/2000
10/10/2000
30/09/2003
18/11/2003
25/11/2003
95/96 - 27
14/04/1996
14/04/1996
EFFECTIVE
_END_DATE
JURISDICTION
COMMENTS
04/08/2005
QLD
In force until new permit being considered
06/12/2003
06/12/2003
NT
NT Collection permits for Casten and Libby
28/04/1996
28/04/1996
TAS
Permit for Quest Trip
Queensland Dept of
State Development
Biodiscovery Act
2000
20/07/2000
20/07/2000
QLD
Biotechnology Benefit Sharing Agreement
DEWHA
(Commonwealth)
EPBC Act and regs
14/07/2008
14/07/2008
AUST
Benefit sharing deed
12
Attachment 2:
AIMS Bioresources Library Field Protocols
Philosophy:
We want to sample Australia’s marine biodiversity, not reduce it.
1. General Rules:
Sample collection may take many forms, and there are different protocols for specific
methods. However, the following general rules apply:
1.1
Quantity:
The collection of any organism must yield sufficient material to
1. provide an appropriate taxonomic voucher for subsequent systematic studies; and
2. Provide at least 4g wet weight for initial chemical extraction, plus, preferably
3. Further bulk sample of 100-400g, to be frozen for follow up chemistry.
Essential requirements (ie 1 and 2) must be met in a single dive. This will ensure
avoidance of rare species.
IF AN ORGANISM CANNOT SATISFY THE ESSENTIAL REQUIREMENTS DON’T COLLECT IT!
ESSENTIAL COLLECTION
REQUIREMENTS
DESIRABLE COLLECTION
REQUIREMENT
TAXONOMIC
VOUCHER
1 Whole individual or
a taxonomically
representative sample.
See voucher reference
table for key
taxonomic parts of
various phyla
BULK CHEMISTRY SAMPLE
SAMPLE FOR
EXTRACTION
4 g wet weight
(approx)
= approx 1cm3 of
dense
organism
up to 400g extra material
400g = 2 clenched fist-fulls of dense
organism
1.2
Taxonomic vouchers:
A voucher must be collected for every sample. To collect an adequate voucher, you need
to have some idea of how the organism is identified (see voucher reference table).
Preferably, the voucher specimen should be the actual specimen photographed, although
in many cases this may be difficult to ensure. The voucher should be a ‘typical’
specimen.
There are three steps in vouchering a specimen: Relaxing; Fixing; and Preserving. Out
of these, only relaxing and fixing takes place in the field, and fixing is by far the most
important. Treat vouchers carefully. When adding the relevant liquid to a live organism,
do so gently. Do not stress it further (and possibly cause retraction or damage, hence
making ID’s difficult) by directing strong jets of fluid onto live tissues.
Relaxing:
When some animals get fixed, they react by contracting and retracting some important
taxonomic parts (eg mouth parts, tentacles). Such organisms include worms, molluscs,
ascidians, and some other soft things. They may be relaxed by adding menthol to
seawater and putting the specimen in the fridge for a few hours. A couple of tiny menthol
crystals is enough in about 200mls seawater. DON’T FORGET ABOUT THEM!
Fixing:
This is the most important step. If the specimen is not properly fixed, then it will
dissolve/collapse/fall apart. Note also that if a specimen is fixed properly and
accidentally dries out at a later date, it will probably still be useful. We use two types of
fixatives: 70% ethanol and 10% seawater formalin. See the voucher reference table for
choice of fixative depending on taxa. Generally speaking, sponges, solf corals,
gorgonians and echinoderms cannot be fixed in formalin and should always be fixed in
ethanol. All other organisms should be fixed in formalin. When fixing, choose an
appropriate sized jar which allows the specimen to be well immersed.
Formalin Fixing:
Formalin is very very toxic, and horrible to work with. Always dispense it in an area well
ventilated with fresh air (eg the back deck). Our method is to place the organism in the
jar with a measured amount of seawater which is enough to cover the sample. (The
organism may need to be relaxed at this point prior to fixing). Then, add enough 30%
formalin to make a final solution of 10%. You will find 3 nappy buckets in a convenient
location. One contains safety gear (goggles, gloves, mask), one a bottle of 30% formalin
with dispensing system, and the third contains a small stock of full strength formalin, for
making up and replenishing the 30% bottle. We now handle 30% rather than 100%
formalin while on the boat for safety reasons. The following table gives seawater: 30%
formalin ratios, but generally, add half as much formalin as seawater to achieve a final
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10% solution. Jars are to be marked “(F)”. Formalin vouchers are then stacked in wide
mouth 30L plastic drums.
Seawater
100
200
300
400
Formalin
50
100
150
200
IMPORTANT:
SAFETY RULES FOR HANDLING FORMALIN
--LOCAL REGULATIONS MAY APPLY- Always choose a well ventilated spot, with the breeze blowing from the formalin away
from you and not over someone else!
 Make sure you are dispensing 30% formalin, and not full strength.
 Wear respirator mask provided.
 Wear disposable gloves provided, and do not re-use.
 Wear safety goggles provided
 In case of spillage, use deck hose to dilute immediately and wash overboard, and use
detergent if necessary. Notify cruise leader and/or skipper if spill is not contained.
 Re-pack safety gear and 30% formalin in respective nappy buckets provided and
secure lids. Formalin contaminates plastic, so take care not to mix buckets and lids (ie.
don’t put safety gear in a bucket which has held formalin).
Alcohol Fixing:
Organisms fixed in ethanol do not require relaxing, so ethanol is added direct to the
sample. The desired concentration of ethanol for fixing is 70%, but because most
organisms that need alcohol contain a lot of water, we use 80-90%. Ethanol is much safer
than formalin to handle, so it can be used in the ship’s lab. It is however flammable, so
mop up any spills immediately and notify cruise leader and/or skipper if spill is not
contained. Be sure to well immerse the specimen in the ethanol solution. Alcohol
vouchers are then stacked in Kirby Boxes.
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VOUCHER REFERENCE TABLE
ORGANISM
WHAT TISSUES TO Relax
INCLUDE IN VOUCHER ?
FIXATION
F=formalin;
E=ethanol
Sponges
Identified by spicules and
skeletal structure.
Collect a
good fistful, including all tissue
types (ectoderm to centre). Note
how its attached to substrate,
and its color in situ.
No
E
Hard corals
Identified by corallites on dried
skeleton.
Collect enough to
show any branching patterns.
No
Freeze, for subsequent
bleaching.
Soft corals
Gorgonians
Identified by internal spicules.
Note whether polyps are
extended, and overall shape.
Include material from all
representative areas, including
branches, attachment, etc.
No
E
Anemones
Collect whole individual.
Yes
F
Zoanthids
Collect several zooids
Yes
F
Sea pens and Jellyfish, other
jellies
including
salps,
ctenophores etc.
Flat worms
Collect whole individual
No
F
Preferably collect 2 individuals ,
although 1 will suffice.
(allows dissection of mouthparts
if necessary)
No
Other worms
again try for 2 individuals
(above)
Yes
Lay out on a piece of
paper impregnated with
formalin and put in
freezer. Be quick, or
they will fall apart.
Transfer to a jar before
they freeze.
F
Crabs, crustaceans
Collect whole individual.
No
Molluscs
Collect whole individual. Soft
tissue is often needed as well as
shell. Note what they are eating.
Yes
F You may want to
slow them down in the
fridge first - less painful
for both sample and you
(may splash formalin)
F
Bryozoa
Morphology of zooid skeleton
used. Only need a small piece.
No
F
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VOUCHER REFERENCE TABLE (CONTD)
ORGANISM
WHAT TISSUES TO Relax
INCLUDE IN VOUCHER ?
FIXATION
F=formalin;
E=ethanol
Echinoderms
Preferably a whole individual.
OR:
Holothurians: slice off good
cross section at oral end (need
test spiculs and feeding
Tentacles). Note cross section
shape, and presence or absence
of tube feet.
Asteroids,
crinoids
and
ophiuroids: leave complete oral
disc plus at least one arm.
Echinoids:
really do need
whole individual
No
E
Ascidians
Solitary:
collect 2 whole
individuals
Colonial:
collect enough to
cover bottom of 250ml jar
Yes
F
Minor phyla
try for at least 2 individuals
Yes
F
Mangroves
collect leaves fruit and bark.
note height and tree/root form
No
E
Algae and seagrasses
Enough to show leaves, runners,
roots
No
2 specimens.
One
soaked in F then dried.
One in E.
1.3 Processing
Processing is best done in a production line. The minimum ideal number of workers is 3.
the more the merrier, and the following 3 jobs can be further sub-divided as necessary.
Before starting:
 Arrange samples in trays or in their collection bags, preferably in order of sample
number. Combine bags of the same thing.
 Set up the video to watch tape of sample collections, as each sample is processed.
 Clear required bench area.
 Clear fridge of unfixed, relaxed vouchers (ie fix them).
 Make sure there are plenty of handy labels, jars, plastic bags, etc.
Job 1: The photographer
 Photograph samples with still camera, and pass to job 2.
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 Liaise with job 3 on field taxonomy.
 Try to avoid getting salty hands.
Job 2: The messy job.
 Empty sample into photographic tray, along with blue underwater label, and pass to
and from job 1 for photography.
 Label the following:
- 1 scintillation vial with bar code label onto glass.
- 1 voucher jar (choose appropriate size) with bar code label on side and lid, and a
water proof label with sample number written in pencil, inside the jar.
- If a micro sample exists, tear off 2 bar code labels and staple to whirl pack, and
pass onto microbiologist.
 Use knives, shears etc to subsample 4-6g of organism, and chop into small pieces, and
place in scintillation vial. Ensure all tissue types are represented in this sample. You
may need to use a hammer and chisel, or the ship’s vice, for heavy shells. Place vial in
tray (in order) in freezer.
 Select appropriate voucher, and place in voucher jar with appropriate relaxant/fixative.
Pass over to job 3 for field taxonomy.
 Bag remainder, with blue underwater label facing out. Remove all air before sealing
bag. Place this bulk sample in freezer.
 Rinse all processing gear in fresh water at the end of a session, and clean the area.
Job 3:
 Fill in all fields on data sheets, using field slate, video, voucher and literature.
1.4 Housekeeping:
No matter how calm it is, the lab and back deck should be secured for rough weather each
night.
In the lab:
 Be aware of relaxing, unfixed vouchers in the fridge. If they’re due for it, fix them.
 Keep the lab organised. Put things back in their right place.
On the deck:
 Unsecured clutter on the back deck is a safety hazard (ie. trips people) and may be lost
over the side. At the end of each dive, put your dive gear into your Nally bin. Put any
loose items away even if they’re not yours.
 Keep your eye on hanging wet suits. We can’t afford to replace them if they blow
away.
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2. Collection Methods:
2.1
Dive collecting:
 Collect in dive teams of at least 2 divers.
 One person is dive leader, handles the camera and data collection, and chooses what to
collect. The second (and third) person(s) collects it.
 The following is the normal procedure:
 choose sample, select blue sample number.
 video sample, with sample number in frame.
 make field notes on slate, including depth, habitat, insitu color and
morphology, substrate, other notes (eg are polyps out), and prelim ID. Use
adjectives to help you remember when we are processing.
 collect the sample and place in zip lock bag with label. remember the
minimum requirement, and target the ideal voucher + 400g (2 fistfuls). see
below for collection etiquette. If micro sample is required, sub-sample
‘cleanly’ a small portion and place immediately into a sterile whirlpack, then
inside main collection zip lock bag.
 It is possible that you may come across more throughout the dive. If possible, put it in
original zip lock bag with label, otherwise start a new bag and combine back at the
boat.
 Don’t forget to take a GPS fix before leaving the site. Remember the name you give it.
 Make note of any prominent features at the site, which may aid re-location.
 Drain excess water from individual collection bags, and keep out of direct sun for the
trip back to the research vessel/base.
 On arrival at the research vessel/base, immediately transfer samples, camera nally bin,
and boat radio into the lab. Do not leave these things on deck or in the sun.
Collection etiquette:
 Where organisms are solitary, collect whole individuals but no more than 10% of the
visible population.
 Where organisms are modular (eg sponges), collect only 30% of any one individual
leaving the holdfast intact. This will avoid mortality.
 When organisms are colonial/encrusting, do not attack in patches, rather collect (and
leave) one large patch.
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Checklist for heading out to do a dive collection:









fuel
radio for each boat
current-line for each team
water for each boat
safety gear (+Oxy-viva, if indicated) for each boat
1 small Nally bin with camera per team
GPS and PDS
everyone’s dive gear
1 mesh carry bag per team, containing slate + a pencil with lead, at least 20 zip-lock
bags, at least 20 labels, and whirl-packs if required.
Post-trip housekeeping:
Vouchers:
Once at the voucher store, the taxonomic samples are sorted and inventoried. The alcohol
gets changed annually with 70% Alcohol to counter evaporation issues. All site and
sample information is entered into the project’s database.
Bulk:
After the field trip the frozen bulk samples are sorted, reweighed and inventoried. They
are either stored in a –20ºC freezer on-site (AIMS), or kept at Townsville Cold-stores for
secure long-term storage. Samples are kept in zip-lock bags in Kirby Boxes.
Extracts:
Micro- and Macro-samples are kept until needed in their scintillation vials in a dedicated
–20ºC freezer on-site (AIMS), usually in their respective solvents.
Microbial samples:
Microbial samples are grown up on appropriate media and purified. A subset of each
strain of interest is cryo-preserved and kept in a –80ºC, or –135ºC freezer on-site.
The remainder is extracted (see “Extracts”).
Images/video vision:
Currently, only colour-slides of samples, taken underwater or on-deck, are scanned into
tiff and jpeg files and linked into our database. In the near future, either digital images
and /or video may also be integrated into the database.
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