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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: August 2013 to July 2016

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
During the last quarter of 2015, Dr. Made Pharmawati and her colleagues focused on analyzing their previous results on DNA barcoding of seagrass species from western, central, and eastern Indonesia. The analyses are still ongoing, and they expect to be able to begin drafting a manuscript in the first quarter of 2016. They are also working on requested revisions to a manuscript submitted to an international journal published in Indonesia on the topic of PCR-RFLP analysis of Enhalus acoroiddes from southeast Bali. Lab work on other seagrass species is also continuing. After gathering samples of Siringodium isoetifolium in the coastal waters off Sanur and Tanjung Benoa, the team collected samples from Serangan, a small island off the south coast of Bali that underwent reclamation in the 1990s. Lab work on DNA extraction has been conducted, along with analyses of the diversity of S. isoetifolium across Bali waters. PCR optimization is now being conducted.

In the upcoming third year of this project, the team plans to host an international conference on marine biodiversity, tentatively set for late October or early November 2016. Their U.S. partner Dr. Paul Barber of UCLA will present the keynote speech and several other potential speakers both from the United States and Indonesia have been invited. The conference website should go online in February 2016. In the first half of 2016, the team will also continue their research on S. isoetifolium diversity. They hope to complete their data analysis on the barcoding of seagrass species so they can begin writing manuscripts.

Undergrad team members conducting electrophoresis

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

Dr. Made Pharmawati explains 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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