|SCOR Working Group 118: New Technologies for Observing Marine Life|
Terms of Reference
Working Group Members
Funding provided by
the SLOAN Foundation's
Census of Marine Life
2002 Working Group Meeting
(28-30 October 2002, Lima, Peru)
Briefs on Technical Areas Not Covered Previously
Dave Mellinger's own work involved the use of passive acoustics to record whale sounds, identify them as to species, and count individuals by tracking position over time with fixed or mobile hydrophones and digital recording tags. Fixed listening stations had been used with both military and civilian sites in the USA, the central Atlantic and Australia. Autonomous hydrophones with beam forming characteristics were positioned in the Deep Sound Channel, singly or in groups of three for target location, and used to record time series of acoustic pressure measurements (5 Hz to 5 kHz) for periods of 3 months to 2 years. These frequencies encompassed the sounds emitted by mysticetes, lower-frequency odontocetes and many pinnipeds. Records were scanned for marine mammal sounds (using automated techniques to recognise calls) and for trends in abundance of calls with season. The method had shown the presence of sperm whales in the Gulf of Alaska and had provided information on seasonal abundance and geographical variation in abundance. Movements had been deduced by comparing occurrence of calls at different listening stations. Future technical needs included satellite data transmission, higher capacity recorders and an extension of the frequency to encompass the full vocal range of whales from 10 Hz to 100 kHz. Also required were better call recognition algorithms, better estimates of the range at which calls could be detected, and improved models (and data) for estimating the number of individuals present at a listening station. Threshold and data compression systems, which were lacking at present, would also be desirable.
Mobile systems included towed hydrophones (100 Hz - 24 kHz) and drifting directional hydrophones or sonobuoys (10Hz - 22.5 kHz). The lower frequency limit for towed hydrophones, which had a range of 5-40 km, was set by towing noise (2 knots and up), which made the technique poor for the larger whales with call frequencies at the lower end of the spectrum. Sonobuoys, which could radio data to a research vessel, had a range of 20 km but could be used in pairs to estimate the location of the whale. Future technical needs included better integration of acoustic and visual surveys, better field tools, better call recognition methods and better statistical methods. A workshop held in November 2002 to discuss these issues.
Digital acoustic recording tags were placed on the outside of the whale with a pole - a difficult technique - and attached with suction cups. The tags, which had a life of only 8 hours, recorded sound (to 8 kHz), depth, pitch and roll and acceleration integrated over several minutes. They had been used to record dive profiles (750-800 m) and the distribution of different calls (regular clicks, creaks, rubbing sounds etc.) during different parts of the profile. Future technical requirements included a tag life ³1 day, a quieter pressure-operated vacuum pump to improve the performance of the suction cups, a 3-D velocity meter and a sensor for body heat.
Molecular tools for analysing marine biodiversity and abundance
The traditional approach to species identification, which was based on morphology, behaviour and ecology, was of limited value for various reasons including lack of expertise and shortage of time. These could be overcome by molecular techniques based on the polymerase chain reaction (PCR) and DNA sequencing. The PCR, which selectively amplifies a target DNA region to 106-109 above background, works with small samples and old, poorly preserved material. The amplification is equivalent to selecting a single sentence or paragraph from a book with 350,000 pages and making several million copies. Synthetic oligonucleide 'primers', 15-30 nucleotides long, anneal precisely to target complementary sequences in template DNA. The primer is extended by DNA polymerase and heating through n cycles to produce 2n copies. Different types of primer provide different levels of identification. Universal primers identify homologous targets in a wide array of species, such as all bivalves; specific primers work only with a selected taxon. The technique, which has revealed a vast, previously unknown, species richness among microbes, is biased against organisms with sequence differences in the primer site and doesn't work with viruses, for which electrophoretic methods provide an alternative.
DNA sequences can be determined directly by automated sequencing, which identifies the entire sequence of the target gene, or indirectly by a number of methods, such as restriction fragment length polymorphism (RFLP), hybridisation probes, DNA arrays, single nucleotide polymorphisms (SNP), and denaturing gradient gel electrophoresis (DGGE). In RFLP the restriction enzyme cuts the DNA at or near the target sequence; an electrophoretic gel is then used to separate cut and uncut DNA. With hybrid probes a synthesised oligomer nests against the matching chromosome sequence and is labelled with fluorescene. FISH (fluorescent in situ hybridisation), for example, detects whole individuals of target microbial taxa. DNA arrays, which consist of small spots of DNA probes on glass, offer the most powerful tool. They can rapidly and simultaneously search large numbers (thousands to hundreds of thousands) of targets and provide some measure of quantity, as well as presence or absence. Cross-hybridisation of probes is currently a problem, as is cost, although competition in the biomedical field is rapidly driving costs down. SNPs are ubiquitous and thousands to millions of samples can be handled in a day when this technique is used in conjunction with temperature gradient capillary electrophoresis (TGCE). These indirect techniques offer the prospect of rapid, standardised identification and classification with no need for taxonomic expertise, although it is probably necessary initially to define how many base pair changes are typical of the differences between species in each taxon. Within a species there is typically 2% variation in a target gene, although there are slight variations between populations in different geographical areas. Automation of the whole process is possible and MBARI is designing a remote environmental sampler, although this may possibly be an unduly complicated approach. SNPs can be used for field studies of larval dispersal, survival and recruitment. They have been used, for example, to discriminate between different populations of oysters and DGGE has also been used for the same purpose. Pyrosequencing can identify small numbers of oyster spat with specific haplotypes from large numbers of samples taken over a wide area.
Some of these molecular techniques can be used for estimating abundance and biodiversity, as well as for identification. Hybridisation probes can be used in conjunction with cell count and fluorescence to measure abundance; quantitative PCR (e.g. Real-time PCR) can be used to determine how many target species are present in a toxic algal bloom, such as a red tide. Biodiversity has been investigated in Limulus populations on the Atlantic coast of the USA and in Patagonian tooth fish in the South Atlantic.
In discussion it transpired that molecular techniques could readily differentiate between vertebrates and invertebrates in fish stomach contents and, with appropriate probes, also identify individual species of prey. The quantitative measurements required to estimate digestion rates would, however, be more difficult. Scales and otoliths presented no problems and samples as old as 100,000 years would be acceptable. The techniques clearly had great potential in the context of the CoML initiative, although there some caveats in relation to taxonomy.
The technology also had important practical applications, because there was a need to identify and measure the abundance of the species of phytoplankton responsible for producing harmful algal blooms, such as paralytic shellfish poisoning (PSP), amnesiac shellfish poisoning (ASP), diarrhetic shellfish poisoning (DSP) and Ciguatera fish poisoning. The issues were the safety of seafood for human consumption and the protection of aquaculture stock. Although it involved bioassays with laboratory mice, monitoring for toxins was a much more rapid process than monitoring for the causative species, for which available techniques were slow (microscopy), inaccurate (clonal and physiological variability in toxicity) or had unknown specificity (antibody & nucleotide probes). New techniques, which avoided the inherent variability associated with the 'standard mouse', involved binding toxins to specific targets and were currently increasing the advantages of toxin testing over species identification. Some of these tests were available commercially (see e.g. MIST Alert at http://www.jellettbiotek.ca/).
The phytoplankton component of these thin layers has been sampled and characterised optically with an autonomous profiler such as ORCAS (Percy Donaghay - Graduate School of Oceanography, University of Rhode Island), which has a vertical resolution of 1 cm. Thin layers affect the structure and dynamics of marine ecosystems and appear to be of very great significance. However, a full understanding of critical scale structures, including function and structure, will only come from an examination of the sea at high spatial and temporal resolution over long periods. This will require the development and application of even better instruments designed to obtain information in all three dimensions and record time changes in the scattered signals. Their value will be enhanced if they are used in conjunction with a variety of high-tech optical instruments.Further information is available from the following web sites:
In special cases, the whole of a stock, or a defined part of it (e.g. the spawning stock) passes a narrow section and, by using stationary sensors with online data availability, can monitored more effectively than elsewhere in their distribution. This situation occurs, for example, with Norwegian spring spawning herring, which spend the winter in very large shoals in the narrow fjords near Lofoten, before spawning along much of the western coast of Norway, and subsequently feeding in the Norwegian Sea. The proportion of the spawning stock that overwinters in Ofotenfjord can now be monitored when it passes through an acoustic fence, erected as a demonstration project across the mouth of the fjord. Currently the fence consists of upward-looking echosounders (38 kHz with a 32° x 8° manipulated beam) and a 200 kHz acoustic Doppler current profiler, combined with a 40-element, 12 kHz sonar directed horizontally from one side of the fjord to the other. The ADCP records the currents and bioflux at the mouth of the fjord, as well as behaviour of organisms (but not zooplankton) in relation to the tidal current. Flux data can be compared with targets tracked through the split-beam of the echosounders. A 32-bit broad band connection is planned to connect the project to the Institute of Marine Research in Bergen and also the Internet. In general, depending on the nature of the task, any kind of sensor (biological, physical or chemical) could be added or substituted, and the fence could also be patrolled by an ROV to provide additional coverage.
Future plans include building a similar fence from northern Norway to Bear Island to monitor the influx of water and biological material into the Barents Sea, whose productivity depends entirely on these inflows for heat and recruitment. The distance is 300 nautical miles and the task is feasible logistically because a gas field (Snøhvit) is to be built in a key area. A number of key research establishments and commercial companies with different technical interests (e.g. acoustics, AUV, ADCP, cabled sensors) are already involved and others may be interested.
State of technologies in developing countries: progress report
In general, developing countries need to increase their technical capabilities and expend more effort on identifying and monitoring key populations and communities in the main ecosystems. To do this, they need to acquire LIDAR, optics, broad band acoustics and other new technologies and, just as importantly, train scientific staff to use them. Developing countries also need to develop co-operative programmes with developed countries, seek funds from international agencies and set up international, multidisciplinary research units, which can use the new instruments and test them in the field in real conditions.
Following its previous meeting in Argentina in 2001, WG118 had initiated a sub-group to assist this process. The aims of the group, which consisted of F. Gerlotto (France), I. Hampton (South Africa), D MacLennan (UK), A. Madirolas (Argentina) and M. Gutiérrez (Peru), were to make an inventory of research programmes, scientific expertise, technology, research vessels and related infrastructure currently available in developing countries. The sub-group had begun by identifying developing countries with marine interests, and grouping them into 11 regions. On the basis of replies to an extensive questionnaire, the group had then produced a series of maps of available resources, which included research vessels, detection technologies, portable oceanographic instruments, scientific expertise, remote-sensing programmes and international agreements for joint research. Historically, a paper by Venema (Successes and failures of fisheries acoustics in developing countries, Fisheries Research, 14, 143-58, 1992) provided a benchmark against which to assess progress.
Whilst the use of acoustics had increased significantly in some developing countries over the last decade, it was still primarily used to assess fish distribution and abundance and it was proving difficult for scientists in developing countries to publish their results. In South America, all countries now used acoustics compared with only half in 1992, although in the Caribbean use was still irregular. In Africa, in contrast, whereas there had been acoustic teams in most countries in 1992 and extensive support from Europe, there were now few practitioners left. Similarly, in Asia, active acoustics teams were confined to Thailand and Indonesia, where previously there had been European support in several countries. Chile, South Africa, Argentina and Peru now had TS programmes, where previously there had been none. In 1992, foreign experts managed most acoustics programmes with the support of a few local staff; in 2002, following training by European nations, there were several national teams in developing countries. Similarly, whilst no developing countries were represented in international acoustic communities, such as the Fisheries Acoustics Science & Technology (FAST) working group at ICES in 1992, participation was now significant, if limited.
Although the group had made good progress with its initial enquiries, much still remained to be discovered and a formal approach was needed to obtain information from several countries.
Self-contained acoustica; measurement systems or 'Black box' technologies
High costs and the need for trained observers have led to proposals to automate the surveys by installing acoustic black boxes on fishing vessels to record the digital signals from commercial echosounders. With calibrated sounders, observers would not be needed at sea and trained staff could concentrate on data processing. Under the ACTIVE proposal, each tamper-proof black box would record continuously and data would be removed periodically, using hard discs. The 25 fishing vessels used in the Eureka surveys sail no less than 900 000 nautical miles each year (equivalent to 130 surveys) and the data collection capacity could therefore be significantly increased. The main problem is that commercial echosounders usually produce a stepped acoustic pulse, rather than the square wave signal emitted by scientific sounders on research vessels. There will also be challenges with data processing and data security, as well as those entailed in securing and maintaining close and sustained collaboration between the scientists and the commercial fishing companies.
The ensuing discussion raised a number of pertinent points. These included the possibility of using a cheap, calibrated single-beam echosounder instead of the black box, the need to quantify (possibly with a multi-beam sonar) the relationship between avoidance and the noise levels of individual fishing vessels and the need to avoid using different frequencies on different vessels.
Activities in Mexico
Research on the fish behaviour was being undertaken in Bahia Magdalena, where small pelagic fish were abundant and where catches of sardine, anchovies and mackerel exceeded 30 000 tonnes per year, mostly caught within the bay itself. The aim was to track the migrations of Pacific sardine (Sardinops caerulus) and the red crab (Pleuroncodes planipes), which had apparently filled the ecological niche previously occupied by anchovy. Bahia Magdalena had semi-diurnal tides, whose range was 2 m. Chlorophyll concentrations occurred at the mouth of the bay with tidal upwelling on a rising tide.
Activities in Colombia
Activities in Venezuela
Phytoplankton studies include comparison of in situ optical and chlorophyll measurements with USF data from SeaWiFs images, in order to correct algorithms used with the SeaWiFs optical sensor. As part of the community study, results of a visual census of Strombus gigas, an endangered species, are being compared with satellite images from Landsat 7 and an important relationship has been found between density, age and the soil substrate. Acoustics have been used since the 1970s to monitor the distribution and abundance of small pelagic stocks, mainly sardines on the northeast coast. Sardines comprise 25% of the catch in Venezuela and about 150 000 tonnes are caught each year. Acoustics are also now being used to survey the fish populations in the Orinoco Delta, a remote region with great fishing potential. Distribution, density and species composition along the estuary all change seasonally.
In future, EDIMAR wants to study the effects of upwelling on the distribution of sardines but this entails working in shallow water (0-20 m), where a research vessel is unable to follow. This is a general problem in tropical waters and EDIMAR is considering the use of LIDAR or imaging sonar. Operating range might be limited with horizontal sonar, however, and during the subsequent discussion a number of other techniques for deploying an echosounder were suggested. These included an AUV, which could be fast and quiet, an unmanned catamaran, and a small manned boat.
Activities in Chile
Fisheries investigations used echo integration to estimate the abundance of demersal species, such as hake, southern hake and hoki and (since 1998) for pelagic species, such as Spanish sardine, jack mackerel and anchovetta. Government to provide fishing forecasts used results. Two research vessels were available for acoustic surveys and some fishing vessels had EK60 sounders; some also had sockets into which scientists could plug an EK500 sounder. The acoustics team consisted of six scientists who conducted acoustic surveys and combined the results with data from oceanographic and ichthyoplankton surveys to produce an integrated analysis. The output was charts of the spatial distribution and abundance of anchovy and sardine, school size and location, and distribution in relation to bathymetry, temperature and salinity. In some instances distribution was influenced by freshwater run-off from rivers. Three-dimensional images of fish schools had revealed that the density of fish in the central hot spot of the school was often twice that of the average density in the school. (Gerlotto, F. & Paramo, J. ( The three dimensional morphology and internal structure of Clupeid schools as observed using vertical scanning multibeam sonar, Aquatic Living Resources, Proceedings of the 6th Symposium on Acoustics in Fisheries and Aquatic Ecosystems, (in press)).
Future needs included the ability to investigate deeper resources, such as dory and orange roughy, and the inclusion of sonar in acoustic surveys to study school structure. It was suggested in discussion, on the basis of experience in Australia and New Zealand, that orange roughy might be identified and differentiated from other species by sonar reflections. Ray bending might, however, present problems with the use of sonar at great depths.