All rights reserved. No part of this publication may be reproduced, distributed, or transmitted in any form or by any means, including photocopying, recording, or other electronic or mechanical methods, without the prior written permission of the publisher, except in the case of brief quotations embodied in critical reviews and certain other noncommercial uses permitted by copyright law. LIPI Press © 2016 Indonesian Institute of Sciences (LIPI) Research Center for Biotechnology Cataloging in Publication Exploring Indonesian Microbial Genetic Resources for Industrial Application/Endang Sukara and Puspita Lisdiyanti (Eds.).–Jakarta: LIPI Press, 2016. xii + 221 hlm.; 14,8 x 21 cm ISBN 978-979-799-864-6 1. Microbes 2. Industrial application 3. Indonesia 660.62 Copy editor : Martinus Helmiawan Proofreader : Noviastuti Putri Indrasari and Sarwendah Puspita Dewi Layouter : Nur Aly and Rahma Hilma Taslima Cover designer : Dhevi E. I. R. Mahelingga First Edition : December 2016 Published by: LIPI Press, member of Ikapi Jln. Gondangdia Lama 39, Menteng, Jakarta 10350 Phone: (021) 314 0228, 314 6942 Fax.: (021) 314 4591 E-mail: [email protected] LIPI Press @lipi_press Contents Editorial Note ..................................................................................................... vii Foreword .............................................................................................................. ix Preface .................................................................................................................. xi Prologue: Research Experiences on the Use of Indonesian Microbial Genetic Resources by Microbiologists at the Indonesian Institute of Sciences (LIPI) Endang Sukara and Puspita Lisdiyanti ......................................................1 Rhizobium, and Its Potential to Support Plants Growth and Improve Soybean Production Harmastini Sukiman and Sylvia J. R. Lekatompessy ............................. 15 Taxonomy, Diversity, and Industrial Application of Acetic Acid Bacteria Puspita Lisdiyanti ...................................................................................... 31 Bacterial Cellulose Ruth Melliawati ......................................................................................... 55 Lactic Acid Bacteria from Fermented Food and Feed Yantyati Widyastuti .................................................................................. 75 Future Challenges of Yeast and the Associated Microbes in Ragi and Tape Atit Kanti .................................................................................................... 91 Oligosaccharides, Its Related Microbes and Enzymes Yopi ........................................................................................................... 115 v Industrial Potential of Rhizopus Oligosporus Endang Sukara ......................................................................................... 135 Amylases of Aspergillus Awamori KT-11 and Its Industrial Uses Trisanti Anindyawati .............................................................................. 155 Collection of Indonesian Actinomycetes and Its Uses Shanti Ratnakomala, Puspita Lisdiyanti, and Yantyati Widyastuti .. 177 Epilogue: Microbiology for Better Future Life Puspita Lisdiyanti and Endang Sukara ................................................. 205 Index ................................................................................................................. 213 About the Authors ........................................................................................... 217 vi | Exploring Indonesian Microbial … Editorial Note As a scientific publisher, LIPI Press holds on high responsibility to provide high-quality scientific publication. The provision of qualified publication is the epitome of our works to participate in enlightening society intelligence and awareness as stated in The 1945 Constitution of the Republic of Indonesia. The edited book, Exploring Indonesian Microbial Genetic Re- sources for Industrial Application offers some important findings on the exploration and utilization on the microbial genetic resources in Indonesia. Through this book, some intensive exploration on micro- bial genetic resources in Indonesia, many new species and even new genus of important microbial taxa have continuously been discovered. This book serves to highlight the significant achievements, especially in the area of microbiology, carried out by the microbiologists in Indonesian Institute of Sciences (LIPI). We surely hope this book could give new insights and infor- mation, especially on diversity of the microbial genetic resources in Indonesia and its potential utilization. As a final note, we would like to deliver our heartfelt gratitude to everyone taking part in the process of this book. LIPI Press vii viii | Exploring Indonesian Microbial … Foreword I am very delighted and I really appreciate this bright initiative of LIPI’s researchers to publish a book entitled Exploring Indonesian Microbial Genetic Resources for Industrial Application. This publication certainly helps LIPI to highlight the work being conducted and sets of achievement reached by LIPI’s microbiologists. I witness that there are number of significant achievements in the area of microbiology carried out at LIPI. The dedication of LIPI’s microbiologists marks a new era for LIPI. The number of international scientific cooperation on exploration and utilization of Indonesian microbial genetic resources has been increasing steadily. Through this cooperation, LIPI has successfully upgraded human resources and research capability. The most important achievement is that through the intensive exploration on microbial genetic resources in Indone- sia, many new species and even new genus of important microbial taxa have continuously been discovered. With this, LIPI has proven a significant contribution to the advancement of science in the field of microbiology at global level. The number of microorganism collection continuously increases, some have been studied for its potential utilization, and some are still awaiting for further studies. Upon this achievement, collection of LIPI is not limited to those of plant specimens at Herbarium Bogoriense, ix living plant species at Botanic Gardens, and the collection of animal specimens at Museum Zoologicum Bogoriense, but also include living microbial genetic resources. It is also important to note that through a hard work and high dedication of LIPI’s microbiologists, we could now demonstrate the future value of microbial genetic resources in supporting sustainable development of the country. I do believe that our microbial genetic resources could provide solution to various problems faced by Indonesia and even other countries. We could demonstrate and offer the usefulness of our collection at the grass root level to support pro poor, pro growth, pro job, and pro green initiatives. It is well-timed for LIPI to search strategic partners to con- vert research output to become outcome and provide impact for Indonesian sustainable economic development. At the same time, it is also opportunity for LIPI to build and establish instrument to conserve and sustain the use of microbial genetic resources. LIPI has storage facilities for the conservation of microbial genetic resources, which is called Indonesian Culture Collection (InaCC) which meets international standard as set out by the Budapest Treaty. With this facility, Indonesia now has a facility which can deposit microbial genetic resources, including patent materials and ready for broader collaboration. Jakarta, 12 June 2016 Deputy Chairman for Life Sciences, Indonesian Institute of Sciences (LIPI) Prof. Dr. Ir. Enny Sudarmonowati x | Exploring Indonesian Microbial … Preface Indonesia is a maritime country sparkled by more than 17,000 islands. Each island is isolated one and another for hundred thousands years. Indonesia is also a volcanic archipelago that forms a ring of fire. Indo- nesia has diverse ecosystem types, ranging from mountains covered by snow in Papua to a deep sea in Wallace Weber imaginary line region. These facts are gifts for Indonesia’s biodiversity as Indonesia becomes a truly mega biodiversity country. In fact, Indonesia is the second largest mega biodiversity country in the world after Brazil. Nevertheless, biodiversity of microbes described by many scien- tists in Indonesia is limited compared to plant and animal biodiversity. The biodiversity of microbes in the country has yet to be explored extensively. Scientific work on Indonesian microbial resources has already been started in late 1800 by Dr. M. Treub at Bogor Garden. However, the information on Indonesian microbial genetic resources is still very limited. Treub himself was a botanist. He, for nearly 30 years between 1880 and 1909, collected and described many micro- organisms such as fungi, microalgae, and bacteria. The work of Treub, however, came to a halt as no one followed on his footsteps. Only a little more than 50 years later, the study on microbes in Indonesia was continued in 1960s by Indonesian scientists. Yet, the progress was slow due to limited human resources and research infrastructure. xi Only in the mid 1990s, the work on microbiology was growing. And just recently, during the last 15 years, exploration on Indonesia micro- bial resources has been accelerated by LIPI’s scientists. Cooperation with Japanese scientists, under the auspice of Japan Society for the Promotion of Sciences (JSPS), Japan Bioindustry