Saturday, 31 October 2009

Juvenile stages of coastal fish (some results)

With all the surface trawls having been completed, we have had a preliminary look at some of our data on juvenile fish stages. During a total of 19 trawls, some 151 taxa were distinguished, photographed and prepared for bar-coding and identification. The taxa ranged from species with potential commercial importance such as scombrids (2 or 3 tuna species), anchovies and carangids (10 kingfish species) to coral reef inhabitants such as parrot fish, rock cods and surgeon fishes. To get an idea of the variety of forms and colours, click on the image below. Any guessed on the species in question? Some are easier to associate to their families than others. If you get it right, we will let you know once identification has been completed.

In terms of juvenile species richness (number of species), distribution and abundance the current cruise data must be interpreted with great care. The number of trawls was relatively low and no attempts have yet been made to link our sample compositions to the physical environment. In order to strengthen the data, samples from previous ASCLME cruises as well as upcoming regional cruises need to be added to the analysis. Nonetheless some patterns do seem to emerge (but for now, need to be treated with a pinch or salt).
The number of species caught in each trawl did not vary dramatically between locations (see below). On average 21 species were distinguished per trawl. The fact that this is only a tiny fraction of the total number of species identified, suggests that we have either seriously under sampled (likely) or that different species are found in different localities (apparently true in some cases). Only a more complete analysis of all data sets will allow for a less subjective interpretation.
While the number of taxa collected show little variation between locations, the number of individuals per unit water volume vary more dramatically (see below). The highest densities of juveniles were generally caught along the Madagasi shelf, with fewer being observed in the Comoros region and the lowest overall abundances along the Mozambique coast. Again, additional samples need to be added to this analysis to see whether this pattern stands up to scrutiny.
The juveniles caught during this cruise will add to a regional juvenile identification guide, will allow us to better understand larval and juvenile origins and dispersal (with the help of genetics) and should eventually allow for more informed regional management strategies (pertaining to commercial fisheries as well as coastal ecosystem health).

Cruise Progress: 30 October 2009

We are now on our last transect off the Mozambique Coast and are slowly making our way back to the Comoros. The past ten days have kept everyone on board occupied with continuous physical, chemical and biological sampling. Since the beginning of the cruise, some 136 CTD and 46 full biological stations have been completed. In addition, one demersal, three mesopelagic and 16 surface trawls were undertaken (see map for CTD stations).
As we are slowly coming towards the end of this cruise, data is being transcribed, the first analyses are being conducted and reports are being prepared. We hope to be able to present at least some preliminary findings before we leave the ship next week.

Wednesday, 21 October 2009

Cruise progress: 19 October 2009

As of yesterday 19th October, transects 10, 3 and 2 have been completed (see also map, blog entry 9-Oct-2009)! Due to some delays with national research permits, more time that anticipated was initially spent in the close vicinity of the Comoros islands. Nonetheless, since then, the first three transects have been completed and we are now on our way back to the islands while undertaking stations on transect 3. To date, physical, chemical and chlorophyll measurements have been obtained at some 39 stations and full environmental stations (incl. zooplankton and phytoplankton collection) at 19 locations. Additionally, one demersal trawl was carried out south of Grande Comore and a total of 12 surface and meso-pelagic trawls.
With the exception of some rough weather and swell after rounding the northern tip of Madagascar, conditions for sampling have so far been favourable. During the latter transect, multi-net deployments were deemed too risky.

Monday, 19 October 2009

The sound of (sound) waves: What is fisheries acoustics?

Fisheries acoustics rely on the physics of sound travelling through water to quantify the distribution of biota in the water column. By sending a signal of a given frequency through the water column and recording the time of travel and the strength of the reflected signal, it is possible to determine the size and location of fish and estimate biomass from the acoustic backscatter. The intensity of the returning echo is a measure of the target strength of a given individual at a particular sound frequency. As a fisheries assessment tool, fisheries acoustics technology is an efficient, non-intrusive method of mapping the water column at a very fine spatial and temporal resolution. It provides a practical alternative to bottom and mid-water trawls. However, validation of fish targets is an essential part of interpreting the acoustic signal for any given location. Output from acoustic surveys can be mapped in relation to bottom habitat type, bathymetry, temperature, time of day etc. The ability to census aquatic organisms are more difficult in deep water as many fish species here lack a swimbladder – the major acoustic reflector in most shelf species.
In its most direct form, we could say that fisheries acoustic produces relative information on size distribution of targets, numbers of organisms in the water column, and estimates of biomass, based on the physical properties of sound traveling through water. However, there are many factors that limit the confidence with which this information can be interpreted into accurate measures of absolute numbers of fish, fish lengths and total biomass.

Acoustic surveys onboard Dr Fridtjof Nansen
Dr Fridtjof Nansen uses ER-60 echo sounders (with ER-60 software) and LSSS (“Large scale survey system”, also called “El-triple-S”) for scrutinizing of echoes. The acoustic transducer is attached to an adjustable keel that can be lowered in rough weather to avoid the damping effect of bubbles. Echo intensities per nautical mile are integrated continuously, and mean values per 1 nautical mile are recorded for mapping and further calculations. The echograms, with their corresponding sA-values, are scrutinized every day. Contributions from the seabed, false echoes, and noise are deleted.
The acoustic survey has been carried out by zigzagging between 50 and 500 meters bottom depth around the Islands, as well as along all the transects (north-south, west-east and oblique transects). Four frequencies are being used (18, 38, 120 and 200 kHz). The survey will target firstly plankton, mesopelagic fish and pelagic fish aggregates. Secondly, the dynamics of the migrating scattering layer and the pelagic layer communities will also be studied in more detail using fisheries acoustic and multinet trawling.
The corrected values for integrated echo intensity are allocated to species according to the trace pattern of the echograms and the composition of the trawl catches. Data from pelagic trawl hauls and bottom trawl hauls considered representative for the pelagic component of the stocks, which is measured acoustically, will be included in the stock abundance calculations.
The echo sounders are watched continuously, and trawl hauls in addition to the predetermined hauls are carried out whenever the recordings change their characteristics and/or the need for biological data makes it necessary. Trawling is thus carried out both for identification purposes and to obtain biological observations, i.e., length, weight, maturity stage, stomach data, and age.

So far the R/V Dr Fridtjof Nansen has undertaken acoustics transects around the 3 Island of the Comoros and Mayotte to determine the distribution and abundance of small pelagic fish shoals. Mid-water trawls have been used on fish aggregations to determine species and size composition. However, very few pelagic shoals have been recorded. Schools of fish have been observed in the surface a couple of times, and we have tried to catch them by rod fishing, but so far with little success. These fish aggregations have not been recorded acoustically either. The reason for this could either be that they are too close to the surface (the echo-sounder can only record fish deeper than 6 m depth, or that the fish swim fast and/or actively avoid the research vessel. Strong scatters of mesopelagic fish have been recorded, but no schools which resemble commercially important species.
The conclusion is that there are very few fish in this area. We keep an eye on the echo-sounder all the time and we will conduct pelagic trawling whenever we see any acoustic signals that are strong enough to suggest higher fish abundance.

author: Katherine Michalsen (Norwegian cruise leader); image: Pascal Cotel.
We also made a post about Acoustic Surveys last year with some other details - take a look at this post on acoustic surveys

Trainees and participants continued ...

Soifa Ahamed Soilihi, I am a former student of the University of Tuléar, Madagascar. After my Master's degree I became Conservationist Agent in the non-governmental organization A.I.D.E (Association of Intervention for the Development and the Environment) in the Comoros. I am the national focal point for Coral reef monitoring. After training in the taxonomy of Holothuridae in the Royal Museum of Central Africa (MRAC) in Belgium, I am now in charge of the research unit for Holothuridae, at the mini laboratory of marine biology of INRAPE with the cooperation of the conservatory of the CNDRS museum in the Comoros.
During this ASCLME cruise, I have gotten a big passion for the marine environment, its biodiversity and the importance of every category: the phytoplankton, zooplankton, fishes and finally the big marine mammals. The necessity of having many researchers in the marine environment is a priority for every country and much more for us the island countries.
My passion, led me to resume my studies and to move towards scientific research of marine environments. I followed two Oceanographic training courses, at MARE (Cape Town) organized by the ASCLME project and at ORI (Durban) organized by the SWIOFP project. Now, I would like to proceed with longer term research projects.
Life onboard the Nansen provides comfort and a productive work environment within a well established and respected program. Every day, the work becomes more familiar and routine. We are working with a focused enthusiasm which one rarely encounters on land. I hope that the ASCLME project will continue to be a key to open opportunities for research on the marine environment for all the countries in this region.

Nicolas Rascle completed his PhD in Brest, France, on the drift of materials at the ocean surface. He then moved to the University of Cape Town 10 months ago to undertake a postdoctoral research on general ocean circulation and its link to the earth’s climate. His research interests include all the physical properties of the ocean near the surface: the temperature, the salinity, the turbulence, the waves… Passionate about diving and spear-fishing, this cruise is also an opportunity for him to gain experience in biological oceanography and fisheries related research. And, as soon as the captain authorizes it, to put on the snorkel and look at what is going on down there.

Friday, 16 October 2009

Trainees and participants continued ...

Jaffar Mouhiddine has a MSc in oceanography, is a teacher and research scientist at the Ministry of Education of Anjouan, Comoros. He is also a member of the national center for scientific documentation and research (CNDRS) of Anjouan. In 2004, he was part of his first cruise, conducting research on the Coelacanth. He attended the ASCLME and SWIOFP training course in South Africa in June / July 2009 because he wants to undertake a PhD thesis on Comoran fisheries. This cruise will give him a lot of experience on the fishes and on the general food web of Comoran waters. He also hopes to be part of the identification and treatment of the samples taken during this cruise, which could help him with his research. Presently, the Comoros are lacking knowledge on fish identification and on fisheries management. He would thus like to gain experience among experienced scientist in South Africa and transfer knowledge back to the young university of the Comoros. E-mail address:

Kate Munnik is a MSc student at the University of Cape Town, South Africa. Her MSc project is focusing on the movement of inshore line fisheries on the west coast of Southern Africa from the Northern Benguela to the Southern Benguela region. Kate’s research interests include physical oceanography, ichthyology and marine biology. This is her first research cruise and she is very excited to learn about all the different sampling procedures across the disciplines. Personally, she enjoys running in the mountains, sushi, rowing, reading and hockey (in no particular order).

Wednesday, 14 October 2009

Trainees and participants continued ...

Soafia Binty Ali is based at the Institut Haleutique et des Sciences Marines (IH-SM), University of Toliara, Madagascar. She completed her DEA (Masters) on identification and distribution (through space and time) of zooplankton that exist in the Toliara Bay. For the preparation of her PhD, she is concentrating on zooplankton biomass in the Toliara Bay. This is the first time that she will be participating in a research cruise therefore it is very important for her because she has the opportunity to see different materials that is not available in her institute. In addition, she is gaining experience in different methodologies. This cruise will help her collect data and will assist her in the comparison of zooplankton between Madagascar and Comoros. She would like to participate in the analysis of the zooplankton samples collected during this cruise. In her free time she enjoys reading, watching movies and playing handball.

Caren George is an intern based at SAEON Egagasini node (offshore) and is awaiting her final results from her MSc. Her project centered on the physical, chemical and biological interactions along the STC to the south of Africa. Her research interests include physical oceanography, biological oceanography and fisheries management. She is in the process of developing a PhD topic which she hopes to start next year. She is very excited to join this cruise and gain experience in fisheries related sampling and participating in an international and multi-cultural research cruise. In her spare time, Caren enjoys relaxing at the beach, rock climbing and yoga.

A demersal trawl south of Grande Comore (Ngazidja)

Part of the cruise strategy is to assess the bottom (demersal) fauna and biodiversity of shallow shelf areas. This is typically done by demersal trawls in areas that are neither too steep and rough nor covered in vulnerable species such as corals. To date, around the Comoros, such habitat has only been found once as the volcanic origin of the islands have resulted in very steep and uneven slopes. To visualise the extreme of the slopes, imagine the ship anchored outside the port of Moroni. While the bow (front) anchor was in 35m of water, the stern (back) of the ship was floating 300m above the bottom.
Our first demersal trawl at 90m depth therefore caused much excitement. Highlights of this trawl were the capture of what appear to be six species of Unicorn fish (Naso sp). While some species such as the humpback unicornfish were easy to identify, others did not agree with all characteristics as provided by species keys. Are there more species in this genus than currently accepted? Only a closer examination of the specimen back at the museum will tell! Below are shown some examples.

Introduction to trainees and participants

Over the next few days, the different research participants and ASCLME/SWIOFP trainees will be given a chance to introduce themselves. Here are the first two:

Charine Collins is a PhD student at the University of Cape Town, South Africa. Her PhD project is focusing on the dynamics of the Comoros Gyre and how it may impact on coral reef biodiversity in the region. Her research interests include physical oceanography, marine biology and ocean modeling amongst others. She would like to gain experience in onboard sampling procedures as well as contribute to the collection of data of which some will be used in her research. On a more personal note, Charine enjoys reading books.

Youssouf Ben Ali abdallâh is a native of the Comoros; he has obtained his diploma in Engineering in Oceanography at the University of Sciences and Technology houari Boumediene of Algiers, Algeria. Youssouf’s main research interests are marine seaweeds. His participation on this cruise is his first experience of this kind. It allows him to familiarize himself with different sampling techniques as well as sampling instrumentation, notably the CTD. This is also a big opportunity for him to discover another universe of marine research as carried out by the famous research vessel, the R/V DR FRIDTJOF NANSEN. He is part of the team lead by Dr Sven Kaehler and it is very important to him to be part of this scientific adventure.

Saturday, 10 October 2009

Identifying fish larvae and juveniles

The management of exploited Western Indian Ocean (WIO) fisheries and reefs is dependent on the reliable identification of juvenile fishes, both to understand their potential dispersal, recruitment and recovery, but also to help understand their importance as a food source to many higher order predators (through gut content analysis).
Typically, juvenile/larval identification is difficult as regional keys and guides are scarce the world over and juveniles and adults often show little resemblance to each other. The ultimate aim of this project is, therefore, to develop an illustrated identification key/database of common juvenile and larval fishes, to facilitate their reliable routine identification in the field.
The Fish Barcode of Life initiative (FISH-BOL) aims to facilitate reliable fish species diagnostics using mitochondrial DNA cytochrome oxidase I (COI) sequences that are kept on a centralised database. By comparing COI sequences from juveniles to those already available from adults, species can be matched and identified. The correctly identified juveniles may then be described and illustrated in a field guide.
The current sampling strategy provides for 10 to 16 surface trawls during this cruise, in coastal and off-shore areas close to the Comoros, Mayotte, Madagascar, Mozambique and Tanzania. To date, two surface trawls have been completed and have yielded some 42 species of juvenile/larval fishes. Once back in the laboratory, barcoding will identify these by linking their DNA sequences to those of existing sequences from a database of adult fishes.
The current study is a part of a regional (WIO) research effort that has previously been collecting samples from throughout the Mozambique Channel. Examples of identified juveniles and their corresponding adult stages are shown in the figure below.

Authors: S. Kaehler & M. Mwale

Friday, 9 October 2009

R/V Dr Fridtjof Nansen off to study the Comoros Basin

Once again the R/V Dr Fridtjof Nansen has left port (Moroni, Comoros), this time for a joint ASCLME / SWIOFP research cruise with excited scientists from 6 nations onboard. The aim of this cruise is to establish for the very first time the physical, chemical and biological characteristics of the Comoros Gyre. The Gyre is an anti-cyclonic eddy that is generally located from 10°S to 15°S and between the north-east coast of Mozambique and the north-west coast of Madagascar. The location of the Gyre is not constant necessitating long transects of about 500 km to either side of the Comoros (see map). A number of recent exploratory cruises, satellite tracking and remote sensing studies have shown the northern Mozambique Channel to be a generally oligotrophic environment that nonetheless supports a large number of fisheries, a high biodiversity and high densities of ecologically important top predators. To date, the processes that sustain the biomass and diversity of this ecosystem are not well understood. It has been acknowledged, however, that the region at a global scale, is physically unusually dynamic and it has been suggested that the observed spatial and temporal variability of the physical environment may well play an important role in enhancing both pelagic and coastal production and the distribution of fish, zoo & phytoplankton and coral larvae.

Since the 6th October, the R/V Dr Fridtjof Nansen has completed acoustic surveys around two of the Comoros islands to determine the distribution and abundance of small pelagic fish shoals. Mid-water trawls have been used on fish aggregations to determine species and size composition and surface trawls to collect juvenile fish stages. Biological sampling to determine the length, weight, sex, and reproductive condition of random samples of selected species was also undertaken at each biological station. But more of this later!
Another important part of this cruise is capacity building of trainees & young scientists. In the next few days you will hear more from them about their experience during the cruise. This is a unique survey that will provide important information for the region, so keep following our blog

Author: Kathrine Michalsen (Norwegian Cruise Leader)

Friday, 2 October 2009

Out-Of-Sequence Posts

Apologies for the out-of-sequence posts below. There seems to be a glitch in the blogger software and dates. We'll restore order as soon as we can!

Situation report from D.F. Nansen 12.08.2009

Dear all,

The R/V Dr.Fritjof Nansen is at 15 08S, 40 57E on station 5 on the second environmental line from the north (line 5 in the Cruise orders). We spent most the daylight hours of 11.08.2009 surveying Nacala bay. Today the wind has subsided and the sea is calmer even in deeper (>500m water).

Both Domingos and Sven have pointed out the utility of samples of the juvenile fish. We therefore did a "blind" haul in Nacala bay, with a small catch of juveniles.

In Nacala bay some few small schools at about 200m depth were observed during daylight hours. The ships crew considered them too small and far apart to have a chance of catching them using the trawl during daylight. Therefore we have no biological samples of the schooling fish, but we have allocated them to the PEL 2 group in the acoustic analysis.

It will be interesting to see if we continue to observed such schools close to shore further south. Hopefully the aggregations will increase so that trawl sampling can be carried out.

In Nacala bay we again observed seabirds (a species of tern), although in smaller numbers than in Bai de Memba. We observed some birds feeding at the surface, but no fast schools of fish at the surface. Humpback whales were also observed, but in smaller numbers than in Bai de Memba. These observations are very qualitative in nature as we have no dedicated observer effort for whale s or birds onboard. There are neither any protocols for conducting such investigations. Therefore it will be impossible to make any kind of quantitative assessment of their numbers. We're only able to detect major changes (ie. No birds or birds present), or new species of marine mammals. However, for future surveys including marine mammal and seabirds observers might considered.

Best Regards

Erik Olsen
Mozambican Scientists on the R/V Dr. Fridtjof Nansen. (L-R): Mauricio Lipassula, Pedro Pires, Isaias Tembe, Martinho Padera


Situation Report, 13 August 2009

R/V Dr.Fritjof Nansen is currently at 15 51S and 40 49E on station 6 on environmental line 4 (number 3 from the north). The weather is very good, it is now almost no wind and the sea is very calm. Our work is proceeding according to plan and we seem to have enough time to cover all our predefined tasks. Whether or not we have time to service the mooring off Pemba will be decided upon when we have finished the pelagic survey and head towards Pemba.

Yesterday we reinterpreted all the acoustic data based on methods and thresholding levels specified by Pascal Cotel who has analyzed the 2008 acoustic data. His input has been very helpful and we are now more confident about the acoustic interpretation, although the differentiation between the PEL 1 (clupeoid) and PEL 2 (scombridae, carangidae) is still difficult as there are few schools observed and the trawl only catch these groups during nighttime. The highest densities are observed close to shore and in bays. Last night (23:00) we had a haul in the bay off Mocambique where we caught various species of scad, anchovies, barracudas and others.

We're also continuing with daytime surface hauls to sample the juveniles.

The last day few whales and no birds have been observed because the vessel has been far offshore in deep waters during daylight hours. To improve bird and whale observations we plan to set our course from the end of the pelagic survey to Pemba close to shore and make a more determined observing effort from the bridge and deck.

- Dr. Erik Olsen

R/V Dr Fridtjof Nansen docks in Diego Suarez

The Research Vessel Dr Fridtjof Nansen docked this morning in Diego Suarez (Antsiranana), Madagascar after succesfully completing the second and last leg of the joint ASCLME, SWIOFP and EAF-Nansen West Madagascar Cruise.

The cruise started on 25 August 2009 in Toliare and surveyed the the southern Madagascar Shelf before following the cruise track shown in the image below. The cruise plan included acoustic transects across the West Madagascar shelf and 11 environmental transects. The first Leg of the cruise ended on 18 September in Mahajanga and the second leg ended today (2 October) in Antsiranana.

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