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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 (amadeus.pribowo@i3l.ac.id) 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

Dr. Pribowo and his team conducted three main sets of activities during the second quarter of 2017. The first centered around studies of lignocellulose enzyme synergism, with the specific subtopics addressed including pretreatment, enzymatic hydrolysis, synergism, and lignin-degrading enzyme producer screening. The second set was focused on looking at microbial biodiversity. As part of this effort, the team has set up seven sets of enrichment studies aimed at trapping microbes with lignocellulosic degrading activity. The identification of microbes continues, and as of mid-July 2017 the researchers had 174 PCR products consisting of 57 filamentous fungi, 106 bacteria, and 11 yeast strains ready for sequencing to identify the species. Up to now, they have deposited more than 900 strains in the i3L microbial culture collection. The third main focus of activity this quarter has been the investigation of metagenomic and bioinformatic activity. The team has samples ready for DNA/RNA extraction for metagenomic sequencing, and they continue to develop an in-house database cataloging lignocellulosic enzymes mentioned in the existing scientific literature.

During the remainder of 2017, the team plans to perform metagenomic analysis, and they have recently communicated with an analytical lab regarding the possibility of sending some of their samples for next-generation sequencing analysis. Co-PI Dr. Irnayuli Sitepu plans to attend a microbiome and bioinformatic training course in China, which should help her in further strategizing on plans for the institute’s microbial culture collection activity and in networking with curators of other culture collections to promote data sharing. Meanwhile, students continue to be heavily involved in the research work on this project, including both student enrolled at i3L and visiting interns. Three new interns will join the team in August 2017, including two from Japan and one from the Netherlands.

One-minute video on the project on YouTube


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