Identify a chief scientist who will be responsible for making onboard decisions related to samples, particularly regarding prioritisation of samples during onboard processing. This will be particularly helpful during busy periods with multiple back-to-back deployments. For 24-hour operations, a second-in-charge must also be identified to cover alternating shifts.

Confirm sampling design meets survey objectives, is achievable with planned equipment and time, and has been communicated to all key scientists and managers. See Chapter 2 for further details on sampling design.

Address fine-scale variation and the need for replication in survey sampling design. Although replication should be considered in sampling design among all platforms (Chapter 2), it is particularly important for grabs and box corers due to the large potential variation in biological and environmental variables across metres to centimetres that may preclude the detection of changes over time (Rogers et al. 2008). Each box core or grab deployment should be treated as a discrete sample (i.e. sub-dividing sample is not replication, nor is the aggregation of samples representative). In addition, the type and size of bedforms present should be considered in the assessment of replicates. For example, a grab may land on the crest of a sand wave, thereby returning a sample that is not representative of the variability of the seafloor at the sampling site. We recommend at least three replicate deployments be undertaken at each station (e.g. Long and Poiner 1994) to enable the quantification of fine-scale variation. When this is not be feasible (e.g. in deeper waters with long deployment times, priority to maximise spatial extent of sampling area), replicates should be collected from a sub-set of stations (e.g. Przeslawski et al. 2013) or appropriate geostatistical methods must be used to estimate grab-to-grab variance (Diggle and Ribeiro 2007).

The most appropriate grab or box corer must be identified to suit the vessel, environment, and scientific objectives (Rumohr 1999). Although this Field Manual does not require equipment that preserves the integrity of sediment samples (e.g. multicorer), the use of such equipment may be necessary if a marine survey has scientific aims complementary to the monitoring program (e.g. characterising infauna or geochemical variables through the vertical sediment profile (Eleftheriou 2013)). The results of some sedimentological and geochemical analyses are sensitive to the manner in which the original samples are collected, handled and stored. Ideally, marine sediment collection for the assessment of sedimentology and biogeochemistry should be carried out avoiding any unnecessary manipulation of the sample that could preclude identification of the surface layers. In order to concurrently acquire the fundamental data identified in this Field Manual (biology, sedimentology, biogeochemistry), the chosen grab or box corer should sample an area of the seafloor at least 0.1 m2 and be able to penetrate 5-10 cm into the sediment (Rumohr 1999, Bale and Kenny 2005). To maintain consistency between sites and repeat surveys, only the top 2 cm should be sampled for sedimentology and biogeochemistry; if the sample is disturbed such that the top 2 cm cannot be identified, we recommend redeploying the gear.

Consideration must be given to the location of the grab or corer during deployment. For deep waters where the gear may be hundreds of metres away from the vessel during sample collection, an ultra-short baseline (USBL) is recommended to identify the true location (Narayanaswamy et al. 2016). If a USBL is unavailable, the angle and length of wire payed out should be recorded so that gear location can be trigonometrically estimated (Milroy 2016).

During the planning phases, taxonomists and museum curators must be engaged to ensure that all biological specimens are appropriately preserved, identified and lodged at national repositories (i.e. museums) if feasible. The appropriate taxonomic resolution at which specimens will be identified should also be determined. Species-level identification may be appropriate for voyages of discovery (Przeslawski et al. 2013) and impact assessments, while family level identifications may be acceptable measures of response to environmental gradients (Olsgard et al. 1998, Thompson et al. 2003, Wlodarska-Kowalczuk and Kedra 2007).

Similarly, contractors or collaborators for sedimentological and geochemical analyses must be engaged if in-house capability is not available, including cost and funding sources for such analyses.

Decide on sediment storage and biological specimen preservation or fixation methods. Sediment samples will need to be refrigerated (for sedimentology) or frozen (for biogeochemistry) while biological specimens will need to be preserved. Depending on the collaborating taxonomists and project objectives, larger or fragile biological specimens may be preserved separately (e.g. ophiuroids) or in a different preservative (e.g. buffered formalin to retain morphological integrity of soft-bodied animals). In addition, staining may be used to aide sorting, although this may hinder species-level identifications. Choice of fixatives, preservatives and stains must be done in consultation with taxonomists, molecular biologists, and biochemists who will be involved in using the samples. See Coggan et al. (2005) and Schiaparelli et al. (2016) for information about appropriate preservatives for a range of purposes (species identification and description, genetic analysis, biochemical analysis).

Ensure adequate work health and safety (WH&S) risk assessments are undertaken regarding correct use of sampling equipment and chemicals onboard (i.e. ethanol, formalin). This should include identifying appropriate storage locations for chemicals, as well as personal protective equipment, ventilation, and first aid kits.

Obtain appropriate permits that may apply to collect specimens. Ideally, all surveys using grabs or corers will have a permit for biological collection. If target samples are sediments for physical analyses (e.g. geology survey), biota will still be collected as part of the sample. Without appropriate permits, biological material simply gets discarded overboard. Permits must be considered not just for collecting activities, but also for sample transport to receiving institutions. For example, scleractinian corals are regulated under the Convention on International Trade in Endangered Species, and there may be restrictions on shipping these taxa to museums or other repositories (especially those overseas) without a permit. See Appendix A for a list of possible permits needed for sampling in Commonwealth waters.

Determine if specialists are needed for gear use. Many grabs and box corers require experience to safely prepare, deploy and retrieve. The details below are not targeted for any one particular equipment or system, and we recommend engaging an experienced crew who have previously deployed similar devices. Refer to point above regarding WH&S, and ensure all gear operators are thoroughly briefed.

Establish a standardized winching process suitable for the chosen gear, as this is critical to maintenance of sample quality. For example, most gear should involve a complete stop and slow lowering for the last few metres. This will reduce the bow wave and associated loss of surface material and reduce the likelihood of raising of the sampler before closure is completed (Rumohr 1999).

Design workspaces and workflows for sedimentology, biogeochemistry, and biological sub-sampling. Each collected sediment sample must be sub-sampled or whole samples assigned to a single discipline because each discipline requires particular methods and preservatives that may interfere with the other. For example, the decomposition of infaunal animals affects organic content and other biogeochemical parameters, but biological preservatives will interfere with many geochemical analyses (Bale and Kenny 2005).

Organise shipment of samples from vessel to repository. If only of a small size, refrigerated and frozen sediment samples may be more cost-effective to be transported as baggage with aircraft passengers in which case airline requirements should be considered. Samples in ethanol or formalin are considered dangerous goods, and associated transport must be arranged. Planning for shipment of samples well in advance of the survey will expedite demobilisation and ensures sample integrity.

Pre-survey checklist

Task Description/comments
Identify onboard chief scientist .
Confirm sampling design meets necessary criteria (e.g. replicates).
Identify most appropriate grab(s) or corer(s) to be used.
Engage taxonomists, curators and contractors. Cost activities.
Determine storage and preservation methods.
Complete WH&S risk assessment.
Decide method(s) for locating gear during deployment.
Obtain appropriate permits.
Document gear specification and establish winch protocols.
Determine if specialists needed for deployment.
Design workspaces and workflows.
Organise shipment of samples.