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Partnerships for enhanced engagement in research (PEER) SCIENCE
Cycle 2 (2012 Deadline)

Connecting science and management through biodiversity research and collaboration

PI: Made Pharmawati (Universitas Udayana)
U.S. Partners: Forest Rohwer (San Diego State University) and Paul H. Barber (University of California, Los Angeles)
Project Dates: September 2013 to August 2015

Indonesian Picture A
Eka Fibayani Imaniar, a fourth-year undergraduate student, harvests seagrasses at Sindhu Beach, Bali under the supervision of I Made Pharmawati, left (Photo courtesy Dr. Pharmawati).

Indonesia has almost 80,000 km of coastline surrounded by human development; almost 50 percent of Indonesia’s 240 million inhabitants rely heavily on coastal areas for their livelihood and as source of protein. More than 60 percent of the population’s protein intake is derived from fish and other ocean-related products. Despite an increasing conservation focus throughout Indonesia, coastal environmental degradation is still growing exponentially and fisheries are still not properly managed. Addressing degradation of key coastal habitats and achieving proper fisheries management are essential in reducing pressures on marine ecosystems and threats to coral reef fish. This project has two primary focus areas. The first is coastal sea grass, a coastal ecosystem that receives little attention but is a critical nursery ground for economically important coastal fisheries. The second is humphead wrasse fisheries, the habitats of an extremely valuable reef fish that is being rapidly depleted throughout Indonesia and the Coral Triangle.
Using genetic methods, the researchers will describe sea grass genetic diversity throughout Indonesia and identify those regions of the country most susceptible to environmental threats, including climate change. The result will be useful in helping marine managers determine which areas need to be prioritized for conservation efforts. The scientists will also investigate humphead wrasse fisheries in western Indonesia, supplementing fisheries data with information on habitat community connectivity and parentage analysis that could aid the Indonesian government in effectively managing these fisheries. This information is particularly important in assuring that the fisheries activities sustainable while at the same time assuring a reliable basis for livelihoods in this area. While many universities and research institutions have started using genetics techniques, Indonesian research capacity in genetics is still relatively small. A key goal of this project is to promote genetic methods, which will provide significant training opportunities to the broader Indonesian scientific community by involving more than 10 universities across the country. By increasing their technical capabilities, Indonesian scientists will be able to increase their involvement in the global scientific community. Thus, this project should help to advance the Indonesian science community while producing scientifically reliable data that will promote the better management of marine environments by conservationists. 
Summary of Recent Activities
From July through September 2014, Dr. Pharmawati and her colleagues allocated a majority of their time to laboratory work aimed at analyzing molecular data. The team had previously finished collecting samples from across Indonesia and will analyze the samples through microsatellite DNA markers.

In regards to team development during the first year, three undergraduate students have graduated and obtained their BSc. There are also three undergraduate students during the second year from Udayana University and Gajah Mada University. Their work focuses on multiple areas including the detection of Enhalus acoroides genetic diversity from Ambon and Sulawesi and the genetic identification of seagrass species using DNA barcoding techniques. The one graduate team member is from Bogor Agricultural University and works on the genetic diversity of Enhalus acoroides from Java and Sumatra.

Academically, a manuscript titled 'Genetic Diversity of Enhalus Acoroides (L.) Royle from Coastal Waters of Pramuka Island, Lembongan Island, and Waigeo Island, Indonesia, Based on Microsatellite Data' which discusses the preliminary results of the genetic diversity and relationships of E. acoroides from three locations representing west, central and east Indonesia was submitted to Advance Science Letter. The team is also registered to attend the STACLIM2014 (International Conference on Science and Technology Applications in Climate Change) Conference, which will be held in Denpasar on 17-18 November and is organized by Universiti Kebangsaan Malaysia. An abstract has been submitted for oral presentation entitled 'Delineating Seagrass Biodiversity through DNA Barcoding: Resolve the Ambiguity of Species Identification.'

Dr. Pharmawati plans to continue laboratory work and refine the results of their data analysis so that the results can be published in higher impact factor journal. The team also plans to attend a bioinformatics and molecular data analyses workshop at SEAMEO BIOTROP (Southeast Asian Regional Center for Tropical Biology) in Bogor in November and is planning a trip to visit their US partner in 2015. 


Undergrad team members conducting electrophoresis

Dr. Pharmawati explains how to prepare reaction mixture for PCR reaction

Dr. Made Pharmawati explaines how to prepare reaction mixture for PCR reaction (Photo courtesy of Dr. Pharmawati)Yunita and Maliza, undergraduate students of Udayana University, doing agarose gel electrophoresis of Enhalus acoroides PCR products of microsatellite DNA (Photo courtesy of Dr. Pharmawati).
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