The collaborative research programs are supported under bilateral and multilateral agreements. Currently the following projects and programs undertaken:

1. Assessment of Coral Settlement and Recruitment Patterns in Relation to Coral Recovery in Tanzania
The research forms part of the Coral Reef Targeted Research and Capacity Building for Management (CRTR) Project. This study aims at elucidating the current (2005-2009) coral settlement pattern and compare it with patterns before the 1998 coral bleaching (Henrik et al., 1998), and during bleaching (Muhando, 2003), hence for the first time, establishing long term temporal trends in settlement patterns in East Africa.

2. Assessment of phytoplankton chlorophyll-a concentration and community composition around Unguja Island, Zanzibar
This study commenced in March 2008 and forms part of the GEF/World Bank Coral Reef Target Research (CRTR) for Capacity Building and Management Project. The objectives of the study are i) Identifying phytoplankton present in the water-column and associated chlorophyll-a concentration ii) Find the relationship between chlorophyll-a concentration and nutrients concentration and the healthy condition of the corals; and iii) Assessing if there are seasonal changes in phytoplankton biomass and community composition at the study sites.

3. Assessment of reef fish along the North East coast of Unguja
This study commenced in September 2007, it is part of the Coral Reef Target Research (CRTR) for Capacity Building and Management Project. The project aims at assessing the fish landed and comparing with underwater visual surveys fish data in the fishing areas. The aim is to correlate what’s in the reef and what’s being caught. A sub project is monitoring reef fish and reef invertebrate abundance and diversity.

4. Measurement of seawater temperature off Zanzibar town – Coordinator: Muhando, C.A.
Measurement of seawater temperature using StowAway Tidbit Temperature Logger tied on a staghorn coral branch at 3-4m deep at on selected reefs was initiated in September 1996.

5. Coral reef monitoring in Tanzania - Muhando, C.A.
Coral reef monitoring programs in Tanzania started in the early 1990s. The main objective was to assess the extent of damage caused by the use of destructive resource harvesting practices, mainly dynamite and drug-nets. The derived information formed the basis for setting up of legislation (control) measures, including development of environmental policies, and preparation of annual coral reef status reports for Tanzania. The Institute of Marine Sciences coral monitoring protocols have been improved in order to include biodiversity assessment. Similarly efforts are underway to improve the Community based coral reef monitoring.

6. Review in coral reef remediation and restoration in the Western Indian Ocean – Muhando, C.A.
Where economic returns permit, coral restoration and enhancement programs have been suggested as one of possible solutions (Bowden-Kerby, 1997; Muhando, 2003). Although restoration and/or enhancement of coral reefs through transplantation of coral fragments have been widely investigated worldwide (Bowden-Kerby, 1997), including East Africa (Franklin et al., 1998; Lindalh, 1999; Wagner et al., 2001; Muhando, 2003), large-scale restoration activity has not been demonstrated, and hence techniques have not been effectively passed over to the local communities, whose participation would make a great impact. We need to understand reasons for failures and success before deciding the optimum procedures for coral reef habitat repair or habitat enhancement involving coral fragment transplantation, addition of artificial and/or natural structures to facilitate natural recovery (i.e., settlement, survival and growth).

7. Phytoplankton and Primary Production Studies in the Agulhas-Somali Current Large Marine Ecosystem - M.S. Kyewalyanga
This is a collaborative research with the Marine and Coastal Management (MCM), Cape Town, South Africa. It is a 3-year Project (2006-2008), funded by the National Research Fund (NRF) of South Africa. It involves conducting cruises in the South African waters; Mozambique waters up to Tanzania waters.

8. Cargill Seaweed Project (Variation in Quality and quantity of the phycocolloid carrageenan in cultivated seaweeds with cultivation period, seasonality, and environmental parameters in Zanzibar). - F. E. Msuya and M.S. Kyewalyanga.
This is a one-year project to assess the impact of cultivation period, seasonality and environmental parameters on the quality and quantity of phycocolloid carrageenan in two commercially farmed seaweeds in Zanzibar, namely, Kappaphycus alverezii and Eucheuma denticulatum. Sampling started on 1st August 2008 and will be concluded in July 2009. The project is funded by Cargill Texturizing Solutions in Baupte, France.

9. Innovation systems and innovative clusters programme-The Zanzibar Seaweed Cluster Initiative. - Dr. Flower E. Msuya.
The project has two components, a) Seaweed soap production through value addition to the seaweed, and b) Seaweed farming
The seaweed farming component deals with introduction of farming of seaweed in deep waters to combat the problem of Kappaphycus die-offs and to increase production through innovation of the farming techniques. The seaweed is farmed in depths of 2-6 m depending on site and tide as opposed to the traditional shallow water off-bottom method. The seaweed grows at higher rates in the deep waters with reduced die-offs. In addition, farmers also harvest fish from basket traps placed under the floating systems.

10. Peri urban mangrove forests as filters and potential Phytoremediators of Domestic sewage in East Africa (PUMPSEA PROJECT)
IMS is participating in the Socio-economics and ecosystem goods and services whose aim is: to compare the available sewage management options from a socio-economic and ecological perspective, and to evaluate ecosystem goods and services provided by mangroves exposed or not exposed to sewage and to summarise the current drivers of mangrove degradation and destruction within the study areas.

11. PAR FISH Crab assessment - Jiddawi, N. S., Aniyar, S., Yahya, S.A.S.
The Project is funded by Sarah Aniyar. ParFish Assessment of handline, basket trap and mangrove crab fishery has been conducted in Chwaka Bay, Zanzibar. Parfish indicates what the optimal level of control (e.g.catch quota, the number of boats fishing or area of refuge) should be, to sustain fish stocks and give catch rates. ParFish is an approach to fisheries stock assessment and a tool for involving fishermen in the development of management actions. It is a particularly suitable methodology for small-scale fisheries in developing countries as it: “Allows a rapid assessment, Encourages participation of fishers, Does not require data recorded over a long time series”. At the centre of ParFish is a software for stock assessment that can use a number of different sources of information including fishermen interviews.

12. “The Relationship between Community-based Organizations and effective management of Coastal and Marine Resources in the Western Indian Ocean Region”
The project is funded by WIOMSA – MASMA grants programme. The project looks at how community based organisation manage coastal resources and the relationship between CBOs and other organisations in the areas as well as the government. Participants: Dr Rosemarie Mwaipopo (Tanzania), Dr Eleanor Fisher (UK), Dr. Flower Msuya (Tanzania), Patrick Kimani (Kenya), Innocent Wanyonyi (Kenya), Vivian Bashemererwa (Tanzania), Joseph Tunje (Kenya)

13. Comparative influence of freshwater-saltwater regime on the ecophysiological functions of the mangroves Avicennia and Heritiera from Ruvu Estuary, Tanzania: an experimental assessment. - Mangora, M.M.
WIOMSA Marine Research Grant (MARG I), 12 months project (revised and extended).
o Field and laboratory work concluded.
o In preparation of final report

14. Carbon and Nitrogen flow in mangrove-seagrass communities subjected to varying levels of human disturbances in Tanzania.- Shunula, J.P., Muzuka, A.N.N. and Mangora M.M.
Sida-SAREC Research Grant. 12 months project but has been prolonged while waiting for results of isotope analysis from abroad.

15. The impact of marine protected areas on the livelihoods of coastal communities: a case study of Mnazi Bay-Ruvuma Estuary Marine Park, Tanzania. - Mangora, M.M., Shalli, M.S. and Msangameno, D.J.
Research on Poverty Alleviation (REPOA) Research Grant, 12 months project (revised and extended).
o Progress report submitted and presented at 13th REPOA Research Workshop in April 2008.
o In preparation for the second phase of field work

16. The impact of seasonal variations in fisheries output on the livelihoods and poverty levels of fishing communities in the Kilombero River Basin, Tanzania. - Msangameno, D.J. and Mangora, M.M.
Research on Poverty Alleviation (REPOA) Research Grant, 12 months project (revised and extended).
o Field work concluded
o In preparation of final report

1. Study of environmental changes in Tanzania coastal waters for sustainable utilization of marine resources and conservation of coastal ecosystem - Muzuka, A. N. N., Dubi, A. M., Nyandwi, N., Masalu, D. C. P., Ngusaru, A., Francis, J., and Shaghude, Y. W.
The project is funded by Third World Academy of Science (TWAS) for capacity building and research. The project started in 2003 and in 2008 TWAS funded this project to the tune of USD 20,000.00. The purposes of the project are capacity building and research on the physical environment of the Tanzania coastal waters and monitor the environmental changes. The main areas of research chosen for the proposed project are climate change and coastal dynamics.

2. Quaternary Sedimentary Record of Monsoon Winds Variability and Associated Carbon and Nitrogen Burial Rates on the East African Continental Margin - Muzuka A.N.N., Shaghude Y.W. and .Nyandwi N.
The study is funded by the UDSM Research and Publications. Sediment cores were collected from the Pemba Channel during the International expedition with RV Meteor in the Tanzanian continental margin. Analyses include grain size distribution, determination of stable isotopes of organic carbon, biogenic composition, etc.

3. Investigations on coral settlement, recruitment, restoration and associated environmental factors - Muhando, C.A., Muzuka, A. N. N., Mohammed, S. M., Mtolera, M. and Machiwa, J.
The study is part of Coral Reef Targeted Research project at IMS. Sediment traps are installed at Bawe and Chumbe Islands reefs and are retrieved and re-deployed once every month for the whole year. Current and waves are also recorded over a year using current and wave profiler.

4. Shoreline Changes in Tanzania and Kenya, Their Socio-economic Impacts and Mitigation Options - Y.W. Shaghude, N. Nyandwi, A. M. Dubi, I.P.L Sanga, F. Msuya and M. Shalli.
This is a multidisciplinary and Regional project involving two study sites, namely Kunduchi (Tanzania) and Shanzu-Bamburi (Kenya). It is a three years project (July 2006 – June 2009) funded by the Western Indian Marine Science Association (WIOMSA) competitive MASMA (Marine Science for Management) grants. Activities of the project include: 1-the supply of sand to the shore zones; 2-the role of monsoonal forcing in shoreline change and 3-the role of tidal currents in shoreline changes. In the end a shoreline changes management manual will be produced.

5. Mapping and Characterization of Coral Reefs Habitats and the Associated Threats - Y.W. Shaghude, C.A. Muhando, M., Shalli, M., Mangora, M.
The research project is part of the multi-disciplinary Coral Reef Targeted Research for Capacity Building and management (CRTR) program, which is sponsored by the GEF/World Bank. The project has two major components; the first one is addressing the concern of establishing a GIS database on coral reef threats in Tanzania and the second one addresses the concern of having an updated information regarding the current distribution of coral reefs and its associated physical and ecological environments using remote sensing techniques.

6. Investigation of the indigenous knowledge on coral reefs management in Tanzania - Masalu, D. C. P. and M. Shalli. This study is part of the CRTR project.

7. Investigation of the global geotectonics of mid-ocean ridges - Masalu, D. C. P. This study makes use of published geophysical data to map past locations and lifting of mid ocean ridges.

8. Western Indian Ocean Climate and Sedimentation (WINOCS) With RV Meteor - A.N.N. Muzuka, Y.W. Shaghude and N. Nyandwi:.
The team of IMS scientists is collaboratively working with German scientists to investigate the past climate as recorded in the sediment of the Western Indian Ocean continental margins. Using the RV METEOR, the scientists have worked at three sites: 1- the continental margin in the northern parts of Tanzania (including the Pemba channel, East of Pemba Island and southern parts of Kenya), 2- the continental margin in the central Tanzania (including the area located south of Unguja Island and the area off Rufiji delta) and 3- the continental margin in the southern Tanzania (including the area off Ruvuma delta). Several long cores (from a gravity corer) and multicore samples (from a multi-core sampler) have been retrieved from each of the three sites for subsequent analyses of the past (Pleistocene – Holocene) monsoon winds variability record.

9. Genetic connectivity and its implications for the design and management of marine protected areas in the East African Ecoregion (WIOMagnet project).
This project is funded by WIOMSA through MASMA grants programme. The overall goal of the project is to assess the population genetic structure of reef associated fish species and reef building hard corals along the Eastern seaboard of Africa and islands of the Western Indian ocean, with the purpose of providing reliable background data pertaining to the level of connectivity across the region and between protected and unprotected reefs. The work is conducted in collaboration with individuals from CORDIO East Africa, Kenya, School of Life Sciences, Södertörn University College, Sweden and Mauritius Institute of Oceanography (MOI).

10. The Potential of Mangrove Systems as a Sink of Anthropologically Derived Nutrients
This project is funded by WIOMSA. The project is investigating the viability of mangrove forests as natural waste treatment systems especially with respect to reducing the nutrient load from domestic waste. It has the following objectives:
1. To determine the physico-chemical characteristics of mangrove sediment at the study area. These will include sediment grain size, organic matter content, and pore water concentration of nutrients
2. To determine input load of nutrients in to the mangrove system
3. To measure lateral fluxes (including loads) of nutrients between mangroves and the receiving water bodies
4. To measure the capacity of sediment to uptake nutrients through measuring nutrient exchange (fluxes) through the sediment-water interface

11. Pollution monitoring in the waters off the Stone Town, Zanzibar under the WIOLAB project.
This ongoing project is part of a region-wide WIO-LaB project that assesses environmental pollution in the coastal zone, including its sources. The project has the following components:
• Identification and assessment of pollution hot spots
• Implementation of a Regional Water and Sediment Quality Monitoring Programme;
• Development of National Pollution Status Report
• Development of water and sediment quality objectives and standards.
Surveys have been carried out in the study area that includes the waters between Bawe island and the shores of the Stone Town. Data collected include water column nutrient and dissolved oxygen levels, salinity and chlorophyll concentration levels. A final report has been submitted.

1. Sida-SAREC Marine Science Bilateral Programme.
The programme is funded by Sida-SAREC. In this programme a key component is capacity building through provision of scholarships for postgraduate studies. The programme also generates scientific knowledge on the Tanzanian marine environment and resources through research by acamemic staff and student projects.

2. GEF/World Bank Coral Reef Target Research (CRTR) for Capacity Building and Management.
Apart from research on coral reef issues including diseases, connectivity, coral diversity, etc the programme intends to build capacity by funding postgraduate research.

In addition to this, support has been provided through various collaborative research programs, which have been, or are, supported by the EU, UNESCO, ROSTA, IOC, UNEP, IUCN, WWF, IFS, World Bank and other international organization.