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Partnerships for enhanced engagement in research (PEER)
Cycle 4 (2015 Deadline)

Developing a bioeconomy in Indonesia: identification of novel microorganisms and microbial enzymes from Indonesian peatland and buffaloes to improve bioconversion of oil palm residues

PI: Amadeus Pribowo ( and co-PI Irnayuli Sitepu, Indonesia International Institute for Life Sciences (i3L)
U.S. Partner: Kyria Boundy-Mills, University of California, Davis
Project Dates: November 2015 - December 2017

Project Overview

4-146 Swamp Buffaloes
Swamp buffaloes cool off in muddy water. They have fewer sweat glands than cattle, and the mud left on their skin helps keep them cool and prevents insect bites. (Photo taken by project researcher Dr. Irnayuli Sitepu at a buffalo breeding center managed by Sumber Alam Ciapus)

The overarching goal of this project is to explore Indonesia’s rich biodiversity in two different ecosystems, namely peat swamp forests and buffalo manure, to find new enzymes and microbes that can improve the efficiency of converting Indonesia’s abundant biomass residues into energy and other value-added products. Indonesia is one of the world’s top biodiversity hot spots, and its microbial diversity has the potential to be a rich source for various biological products such as novel pharmaceuticals or industrial enzymes. Unfortunately, much of this microbial biodiversity remains unknown to science due to the insufficient research funding and capabilities in Indonesia. This project aims to build technical capabilities in metagenomics research to explore the microbial diversity of Indonesia and build a culture collection to facilitate ex-situ conservation of this microbial diversity. In addition, research will focus on identifying novel enzymes to improve the bioconversion process. Microbial communities living in peat swamp forests and buffalo manure are likely sources of novel enzymes that can break down lignocellulose, the fibrous material in plants. The high proportion of lignin in peat (Factors, 2015) may naturally promote the selection of microbial communities that can degrade or modify lignin. Similarly, a recent study has discovered vast arrays of enzymes that are active on lignocellulosic biomass from buffalo rumen (Duan et al., 2009). As buffaloes can thrive on low-quality feeds that are hard to digest (Bilal et al., 2006), the microflora living in the buffalo rumen are a likely source for enzymes that can effectively break down hard to digest biomass materials. To date, no studies have been done to thoroughly explore the potential of microbial enzymes from these two ecosystems for improving the efficiency of the bioconversion process. As a third objective, the researchers will also work to identify yeasts that can convert lignocellulosic sugars to oil for biofuels.

The development benefits of this project include promoting conservation of Indonesia’s biodiversity, strengthening education and research capacities, facilitating climate change mitigation, and supporting green economic development. As an agricultural country, Indonesia has enormous biomass resources, but most of these biomass residues currently go to waste. On the other hand, Indonesia is highly dependent on fossil fuels, which account for more than 95% of Indonesia’s total primary energy mix (National Energy Council, 2014). Biorefinery technologies can turn biomass residues into products such as biofuels, biochemicals, and electricity. Hence, developing biorefineries to create value-added products from Indonesia's biomass resources can help reduce the country’s dependence on fossil fuels, reduce green house gas emissions, create jobs, and promote rural development. Efforts to build biorefineries have so far been hampered by the high cost of enzymes. This project aims to overcome this challenge by utilizing local biodiversity to find novel enzymes and microbes that can lower the cost of the bioconversion process or facilitate the production of new products.

Summary of Recent Activities

In his final report on this project, when ended as of December 31, 2017, the PI Dr. Pribowo notes that this PEER award represented his institution’s first foreign funding and its biggest grant overall since i3L was founded about five years ago. He also notes that the project has helped i3L internally to become more confident in leveraging research and development activities as part of the university’s mission. It has also facilitated the involvement of students in a real research setting beyond what the students received in class, and it contributed to the educational process especially in the laboratory practice. Several students were funded to attend professional and academic conferences, where they presented their results from the project, giving them the opportunity to develop their soft skills as young scientists.

On the research side, the project has helped in implementing and improving techniques and methods that otherwise might be impossible without the PEER support. The instruments purchased during this project will continue to be utilized by i3L and others. For example, the thresher that was used to thresh biomass is now being used for processing organic waste as part of the waste management initiative at i3L. The PEER support also helped create a microbial culture collection at i3L. Building a culture collection was not part of the initial activity plan, and the PI and his team originally planned to collaborate with a local microbial culture collection to jump start the process of enzymatic screening while gradually collecting microbes from the environment of interest. However, we could not secure any collaboration, mostly due to restricted use of the other collection for internal research. Buying microbial strains was not an option due to the expense. Therefore, the team focused their first efforts on collecting microbes. As a result, PEER funding was crucial in the establishment of a collection with more than 1,200 strains as of January 2018. The researchers are in the process of uploading a set of 231 microbial strains into the Global Catalogue of Microorganisms. This open catalogue allows global communities to access the team’s selected microbial database and communicate with them if there is any interest in the microbes. This Global Catalogue of Microorganisms is managed by the Chinese Academy of Sciences and can be accessed from and The registration ID is i3LCC WDCM1137 - i3L Microbial Culture Collection Indonesia International Institute for Life Sciences (i3L).

Although the project ended about a year early due to job changes by the PI and co-PI, Dr. Pribowo reports that he and his colleagues plan to continue their research on potential microbes and enzymes with elevated levels of lignocellulosic enzymatic activities. They also intend the continue exploring possible utilization of i3L’s microbial culture collection and its team’s capacity in metagenomics for other applications (for example, in healthcare or food science). They university is able to provide a small grant to continue the research project even now that PEER funding has ended, and the team is also actively looking for other research grants. They remain in collaboration with their U.S. partner Dr. Kyria Boundy-Mills in preparing manuscripts for publication.

One-minute video on the project on YouTube

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