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Progress Reports


Four US students and their US advisors Dr. Jurgen Theiss, Dr. Javier Zavala-Garay, and Robert Thombley were hosted by the Institute of Marine Sciences (IMS) in Zanzibar during July and August 2009. The students summarized their work and results in a progress report.


The Regional Ocean Modeling System (ROMS) model of the Zanzibar Channel developed by Gabriela Mayorga-Adame in 2007 (see below) was further developed by Shigalla Mahongo of the Tanzania Fisheries Research Institute (TAFIRI), Tanzania, during his one-month ROMS training provided by Dr. Javier Zavala-Garay at Rutgers University, USA, in July and August 2008. Mr. Mahongo's visit was supported by a POGO-SCOR Fellowship (Grants and Contributions). The model is forced at the boundaries by the annual cycle of HYCOM at 1/12° resolution. It is forced at the surface with the annual cycle of winds stress and surface heat fluxes derived from the meteorological station in Zanzibar. The initial condition was derived from HYCOM and after one year of adjustment it reached a steady state describing the annual cycle. The annual cycle could not be verified or studied during the visit.

Further information: Mr. Mahongo's final report on his visit.


A ROMS model of the Zanzibar Channel was set up by Gabriela Mayorga-Adame during her two-week visit to Theiss Research in La Jolla, CA, USA and the subsequent three-month visit to the Institute of Marine Sciences (IMS) in Zanzibar, Tanzania, from April to July, 2007. These visits were funded through the NSF/OCE grant of Dr. Jurgen Theiss (Grants and Contributions). As initial conditions for her model, Mrs. Mayorga-Adame assumed constant temperature and salinity throughout the channel and the northern and southern channel entrances to be open boundaries. She found that the dynamics of the Zanzibar Channel is distinctly different during the two phases of the monsoon by simply considering constant wind forcing, using a typical speed and direction during the peak of each of the two monsoon phases, respectively, as measured by a meteorological station in Zanzibar. She also showed that the model reproduces the general feature of the observed tidal dynamics.

Further information: Gabriela Mayorga-Adame.

Originally Proposed Research

The Zanzibar Project from 2009 to 2011 is entirely funded by the NSF/OISE IRES grant (Grants and Contributions) in order to give undergraduate and graduate students in the US (below referred to as 'students') an international research experience. The following are extracts, slightly revised, from the original proposal of February 2008 that lead to this grant (Original proposal - project summary and description only). The actual research might somewhat differ from and hopefully surpass the research that was originally proposed.

Modeling Projects

Tropical Western Indian Ocean Model. This line of model study involves the consideration of the large-scale dynamics that affects the Zanzibar Channel, most notably the East African Coastal Current (EACC) described in section 'Zanzibar Channel'. The students will therefore study the large-scale dynamics given by the output of the ROMS model of the tropical western Indian Ocean. This model was recently developed by Prof. Chris Reason, who will guide this study, and his postdoc Dr. Juliet Hermes (Hermes and Reason, 2008). To obtain an understanding of the accuracy of the model output the students could compare it with data available for the open ocean, for instance, through HydroBase, from ALACE floats (Chapman at al., 2003), and ARGO floats. Since the focus is the effect of the large-scale dynamics on the Zanzibar Channel, it might become beneficial to re-configure the model appropriately and re-run it. This would also be a good learning experience for the students as they could familiarize themselves under the supervision of Prof. Reason how such ROMS models are set up. The re-run can be done at no cost to the proposed project on the computer cluster of Dr. Emanuele Di Lorenzo. Ultimately, these proposed activities should provide initial and boundary conditions for the model of the Zanzibar Channel, which is described next.

Zanzibar Channel Model. This line of model study is to generalize Mrs. Mayorga-Adame's model setup above with the aim of producing an annual cycle. The wind forcing will therefore be chosen to be again constant in space but annually varying in time. The annual signal will be extracted from a ten-year wind data record from three meteorological stations along the coast of the Zanzibar Channel. Similarly, nearby data points from NCEP or ERA40 heat and freshwater fluxes will be used to determine a surface forcing that is constant in space and annually varying in time. It is worth noting that precipitation varies significantly annually ranging from 47mm (July) to 401mm (April) (WMO website) with the two rainfall seasons being March-May and September-November due to the movement of the ITCZ. Since no major river empties into the Zanzibar Channel, fresh water input through rivers appears unlikely to be a dominant forcing. Because no published data appears to exist local knowledge will be sought. Mrs. Mayorga-Adame's initial condition of a constant vertical temperature and salinity profile could be replaced by exponentially decreasing one, by one from the above-mentioned tropical Western Indian Ocean model, and eventually by the one measured by the data projects described further below. Boundary conditions at both channel entrances will be provided by the tropical Western Indian Ocean model, whereby the effect of the EACC will be particularly important. This is because the observed average speeds of the portion of the EACC flowing through the Zanzibar Channel range from 0.25m/s to 2m/s (Newell, 1957) and thus the lower end of the range is comparable with the range of speeds generated by Mrs. Mayorga-Adame's model that did not include the EACC.

A series of studies will be carried out to determine the relative importance of the various processes. Of particular interest will be to determining whether the EACC alone causes a total mass flux through the channel or whether local wind forcing or other processes are contributing significantly as well.

One of the applications of the model is to understand dispersion of pollution and coral larvae. The latter is also of particular interest to the World Bank's Coral Reef Targeted Research and Capacity Building (CRTR) Program, which is one of the Zanzibar Project's partners. It is therefore proposed to track numerical particles as the model is being refined.

Data Projects

The data projects will measure velocity, salinity, temperature, and pressure in the Zanzibar Channel, which is virtually unexplored in this regard. This represents a unique opportunity for the students since they can learn about standard measurements and at the same time produce new results worth publication. Such a combination is hard to find along the United States coast where standard measurements most likely have been taken already.

The Scripps Institution of Oceanography (SIO) is kindly providing an ADCP and a CTD to the proposed project at no cost. The ADCP measures continuously bathymetry and vertical profiles of velocity during the planned cruises and the CTD measures at certain locations vertical profiles of salinity, temperature, and pressure. IMS in Zanzibar has recently ordered two different ADVs and a CTP recorder. All three instruments are designed to be moored. The two ADVs measure velocity, temperature and pressure and the CTP recorder salinity, temperature, and pressure. IMS in Zanzibar will also provide their research boat. This boat, however, is not fit to venture near the entrances and certain other parts of the Zanzibar Channel and therefore IMS in Zanzibar and the Zanzibar Project will jointly rent a more suitable boat for cruises in these regions.

Dr. Yohanna Shaghude, a senior scientist at IMS in Zanzibar, has already conducted cruises in the Zanzibar Channel and therefore will act as chief scientist of the proposed cruises. The first year will be particularly challenging because the ADCP and CTD will be brought to Zanzibar and used there for the first time. Since the same cruises will be carried out each year it is particularly important that the use of the ADCP and CTD is perfected and documented as much as possible in the first year. To this end, Robert Thombley, a technician at SIO, will therefore visit IMS in Zanzibar for two weeks in the first year.

The students, Mr. Thombley, and anyone else involved can go on the field cruises but must sign a waiver stating that they do so at their own risk. This was suggested to Dr. Jurgen Theiss by Dr. Wayne Patterson at NSF. Mr. Thombley already agreed to this arrangement and Dr. Theiss will only consider student applicants if they also agree to this arrangement. In the event that a student does not want to go on field cruises although the student agreed originally, the student can still gain valuable experience by being involved in the cruise planning, instrument preparation, and data analysis, or by being re-assigned to a modeling project.

Three measurement campaigns are proposed:

Central Transects. Cross-channel ADCP transects and various CTD casts directly from Zanzibar Town are proposed. They will provide the needed data for the model and also have two practical advantages. One is that the starting point of the transect would be just outside IMS thus avoiding a transit. Another is that most of the central part of the channel is quiet. Therefore, the research boat of IMS in Zanzibar, at no cost to the proposed project, can be used and measurements are also easier to conduct. Cruises will be carried out during the day whenever possible. A more suitable boat will be rented to make measurements where the research boat of IMS in Zanzibar cannot go.

If time and resources allow, the transect and CTD casts can be repeated more times to obtain a better average and measurements along different cross-channel transects can be made to obtain information about the horizontal variability.

Northern and Southern Transects. Dr. Shaghude has already conducted bathymetry measurements and collected sediment samples in the central channel (Shaghude and Wannäs, 1998). He is currently planning on doing the same in the northern and southern channel in the next few years while the students are there. He submitted a proposal on this to the Western Indian Ocean Marine Science Association (WIOMSA) in November 2007. This will be a good opportunity to also make measurements with the ADCP and CTD. A more suitable boat for these measurements will be rented jointly.

Moorings. IMS has made no plans yet where, when, and for how long, it will moore the above-mentioned two ADVs and the CTP recorder. It would be an additional experience for the students if they were moored or retrieved while the students are there so that they can participate in their preparation and deployment.

The measurement campaign in the central channel will produce a vertical profile and if time and resources allow also a horizontal section of velocity, salinity, temperature, and pressure with the tidal signal averaged out as well as is possible. This will provide an initial condition for the model. A first rough validation of the model output would be to compare its total mass transport through the channel with these observations. If these quantities are in good agreement more elaborate validations can be made. The measurements in the northern and southern part would provide bathymetry data at a higher resolution than the current one as well as vertical and horizontal sections of velocity, salinity, temperature, and pressure. The moored instruments would provide a time series of velocity, salinity, temperature, and pressure with which the annual variability produced by the model could be validated.

The proposed project will last for three years, which provides the opportunity to repeat the above measurements each year in the same month and thus an average could be obtained. An alternative would be to make these measurements in a different month each year or in at least one year. This would depend whether students would be available if it is not the summer months.

Environmental Context Projects

The development of a model of the Zanzibar Channel and the required collection of data is driven by the need to better understand some of the urgent issues affecting the Zanzibar Channel. One is pollution, especially from the rapidly growing city of Dar es Salaam, the capital of Tanzania. The model would help to understand better its dispersion in the channel. Another one is beach erosion, which is particularly serious just north of Dar es Salaam and is affecting the tourist industry there. The model study and data collection will contribute to data and training tools of the Tanzanian component of the capacity building program of the Intergovernmental Commission (IOC), and other regional initiatives such as the Kenyan-Tanzanian shoreline change project. A third is the general health of the fragile marine ecosystem in which coral reefs play a vital role. This third issue is also of global importance as there are only few areas in the World Ocean covered by coral reefs, which are the richest repositories of marine biodiversity, and this area is shrinking due to economic development and global climate change. World Bank's Coral Reef Targeted Research and Capacity Building (CRTR) Program, a partner of the Zanzibar Project, is a global network addressing this issue. IMS in Zanzibar is a Center of Excellence in this network. The model aims at eventually helping the CRTR program to understand how coral larvae are being dispersed.

There will be no separate environmental context projects to be carried out by students. However, the students will nevertheless learn about the environmental context to better understand the long-term goal that is the motivation for their focused work on the modeling and data projects. This understanding will be developed by speaking to relevant experts not only at IMS in Zanzibar but also at other organizations nearby. Dr. Theiss is already in contact with such experts at the Tanzania Meteorology Agency in Zanzibar, the Faculty of Aquatic Sciences and Technology (FAST) of the University of Dar es Salaam, and the Tanzania Fisheries Research Institute in Dar es Salaam. Contacts to the Marine Parks and Reserves Unit and the Tanzania Coastal Management Partnership (TCMP) still need to be made. Furthermore, if relevant workshops or symposia are held by IOC or the Western Indian Ocean Marine Science Association (WIOMSA) in Zanzibar or nearby the students will be encouraged to participate. These activities will not only give the students a general understanding of the environmental problems that the region is facing but also help them to refine the objectives of their modeling and data projects.

© Theiss Research, La Jolla, CA, USA, 2006-2011, Contact: Jurgen Theiss at