Identify a chief biologist or ecologist who will be responsible for making decisions related to samples onboard, particularly regarding prioritisation of samples during onboard processing. This will be particularly helpful during busy periods with large hauls or multiple back-to-back tows. If 24-hour operations are planned, a second-in-charge will be needed as well.

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. If the study area is small with respect to the size of the combined length of all transects, then the sampling design may be better suited to transects, not points (see Foster et al. 2019 and Chapter 2).

Consideration must be given to the location of the trawl or sled during deployment. Ultra-short baseline acoustic technology (USBL) is recommended to identify the true location of the sled/trawl during bottom contact (Schlacher et al. 2007), particularly in deep waters where the sled/trawl may be kilometres away from the vessel during a tow (Clark and Stewart 2016). If a USBL is unavailable in deep waters, the angle and length of wire payed out should be recorded so that sled/trawl location can be trigonometrically estimated (Milroy 2016). Station record forms should record gear location wherever possible, with vessel location recorded as a back-up.

Consideration must be given to the stability of the trawl or sled during deployment. Ideally, a Netsonde or bottom contact sensor will be used to indicate when the gear is lifting off the seafloor so that speed can be reduced or more wire payed out or retracted. With trawls, door-spread or wing-end sensors are also useful to ensure consistency of gear set-up and performance. If these are unavailable, strict attention must be paid to the winch wire and constant adjustments performed or a self-tensioning winch used to ensure continuous bottom contact (Clark et al. 2016).

During the planning phases, taxonomists and museum curators must be engaged to ensure that samples will be appropriately identified and preserved and voucher specimens are lodged at national repositories (i.e. museums). They can also advise on the likely species selectivity of the proposed gear for certain taxa. Preferably, taxonomists will participate in marine surveys in which case they can identify much of their respective groups onboard (Zintzen et al. 2011). The appropriate taxonomic resolution at which specimens will be identified should also be determined. Species-level identification may be appropriate for voyages of discovery (Poore et al. 2015), while family level may be suited for measuring relationships with environmental covariates (Hirst 2006). For many surveys, identifications will only target selected groups (e.g. sponges in Przeslawski et al. 2015). This should be decided in the pre-survey planning stage, not after sampling has been undertaken. Importantly, non-target specimens should still be retained for museum lodgement if possible, in order to facilitate identification in the future if resources or priorities allow, particularly in locations that are infrequently visited (e.g. deep sea).

The purposes of biological samples must be determined. For monitoring purposes, samples of each target species or operational taxonomic unit (OTU) must be collected for taxonomic identifications. Further objectives specific to a given survey or project may also include samples for genetic or biochemical analyses for particular groups. Protocols for these samples (including preservation as per point below) must be developed prior to the start of the survey.

The level of onboard searching and sorting should be decided during the planning phase** **where there is sufficient information to inform discussion of likely catch rates. Onboard searching refers to the time spent looking through non-biogenic material to find biota, while onboard sorting refers to the taxonomic level to which biota are identified. Both will be determined by the key survey objectives, onboard taxonomic expertise, and available time and space. It is important that search effort is not adjusted between deployments as this is a source of variation in the resulting data. Onboard sorting may vary among groups (i.e. many fish may get sorted to species while invertebrates stay in coarse groups). At a minimum, samples should be sorted onboard by phylum to ensure correct preservation and assist dissemination post-voyage, but samples should also be able to readily be subdivided for many phyla (e.g. Cnidaria, Arthropoda, Echinodermata). Taxonomists are far more likely to be willing to engage in post-survey identifications where the sample has been sorted to an appropriate level onboard.

Decide on preservation methods. This should be done in consultation with curators, taxonomists, molecular biologists, and biochemists that will be involved in using the samples. See Coggan et al. (2005) and Schiaparelli et al. (2016b) for information about appropriate preservatives for a range of taxa and purposes (e.g., species identification and description, genetic analysis, biochemical analysis), noting the variation between taxa.

Ensure adequate risk assessments are undertaken regarding safety and use of chemicals onboard (i.e. ethanol, formalin), abiding by relevant state and federal legislation. This should include where appropriate onboard storage for chemicals, as well as personal protective gear, ventilation, and safety data sheets for hazardous chemicals.

Determine if specialists are needed for gear use. Many nets and sleds require experience to prepare, deploy and retrieve. The details below are not targeted for any one particular equipment or system or item, and we recommend engaging an experienced crew who have previously deployed similar devices.

Obtain appropriate permits that may apply for collection (Appendix B). Ideally, all surveys using sled, trawls or dredges will have a permit for biological collection, even if target samples are rocks and sediments. This will ensure incidental biological specimens do not get discarded overboard. Current regulations require permits for biological material being deposited in registered institutions. For Commonwealth waters, these include

  1. Australian Fisheries Management Authority (AFMA) “Application for Scientific Permit”
  2. Parks Australia: “Application for a permit to access biological resources in Commonwealth areas”
  3. Parks Australia: “Application to Conduct Research Activities Within Commonwealth Marine Reserves”

State-based permits may also be required. For example AFMA have delegated authority in offshore areas of New South Wales and Queensland waters to the states.

Collection ethics approval may also be required from the research institution. In addition, more focussed permits including animal ethics may be needed for particular taxa (e.g. fish and cephalopods). Permits must be considered not just for collecting activities, but also for shipping and storage (e.g., biosecurity containment facilities). For example scleractinians, antipatharians, and some fishes are regulated under the Convention on International Trade in Endangered Species (CITES), and there may be restrictions on shipping these taxa to museums or other repositories (especially overseas institutions) without a permit.

Document the specifications of all sampling gear to be used, including photographs (see Equipment). Specifications that should be documented include gear size and configuration (mesh, floats, ground ropes, frame, spread between trawl doors), rigging plans (bridle, headline layback), and deployment needs (wire length estimated, required towing speed, netsonde or USBL methods). This can assist with estimating location and area of the seafloor sampled, as well as providing crucial information for comparisons with other surveys. Where possible, the gear set-up and specifications should be standardised across all surveys using the same equipment.

Decide on procedures for very large hauls. Sub-sampling or a focus on key taxonomic groups may save time needed for other survey operations (e.g. multibeam mapping) or objectives (e.g. biodiversity characterisation in a different location) (Shimadzu and Darnell 2015). Alternatively, coarse level estimation of abundances could occur based on visual estimates or case counts. Such procedures must be decided before gear deployment and remain consistent for a given survey, and in all cases, representatives of all taxa should be collected and appropriately preserved. If time permits, pilot deployments can help determine the efficiency of the gear, deployment times, suitability of terrain, catch sizes over distances, and processing times.

Organise shipment of samples from vessel to repository (e.g. museum). If samples are frozen and are not too bulky, it may be most cost-effective to have individuals transport them on aircraft in which case airline requirements should be considered. If samples are in ethanol or formalin, transport of dangerous goods must be organised. Planning for shipment of samples well in advance of the survey will expedite demobilisation and ensures sample integrity. The destination museum can likely provide advice on shipping methods and regulations. See Schiaparelli et al. (2016b) for shipping advice.

Pre-survey checklist

Task Description/comments
Identify onboard chief ecologist/biologist
Confirm sampling design meets necessary criteria (e.g. randomised, sufficient number of samples)
Engage taxonomists and curators
Determine onboard sorting level
Determine preservation methods
Complete necessary risk assessments
Identify specialists needed for gear configuration and deployment
Data storage needs identified and hardware purchased accordingly
Decide on methods for locating gear during deployment
Decide on methods to assess gear stability during deployment
Obtain appropriate permits
Document gear specifications
Determine procedures for large hauls
Organise shipment of samples