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Cycle 5 (2015 Deadline)

Enhancing research capacity through a biotechnology-driven investigation of novel Gram-negative bacteria from Indonesian sponges

PI: Ocky Radjasa (, Diponegoro University
U.S. Partner: Phillip Crews, University of California, Santa Cruz
Project dates: December 2016 - May 2020

Project Overview:

5-215 Field Training
The team pauses for a group photo during a field expedition to collect samples in May 2017 (photo courtesy of Dr. Radjasa).
This team’s hypothesis is that an experimental design based on so-called “integrative chemical biology” will provide new insights to better describe life processes in Oceana. This project will leverage an existing Indonesian-U.S. collaboration to make advances in marine microorganism biology, stimulate chemistry discoveries, and engage in outreach to STEM students. The focus will be on using biodiverse Indonesian sponges as a source of new halotolerant Gram-negative bacteria. The project will be based at Diponegoro University (UNDIP, Indonesia) and will be led by Prof. Radjasa, working in cooperation with the natural products lab team of Prof. Crews and leveraging his National Institutes of Health-sponsored project “Merging Marine-Derived Natural Products With Experimental Therapeutics.” The goals are (1) to leverage the aims and expertise of the Crews group to forge a marine sponge-inspired initiative with the Radjasa group at UNDIP; (2) to isolate, characterize, and culture at least 30 strains of Gram-negative bacteria from Indonesian marine sponges; (3) to discover at least 10 novel secondary metabolite scaffolds through the culturing of chemically prolific microorganism strains; (4) to establish a productive research partnership between scientists at UNDIP and UCSC through exchange visits; and (5) to play a part in USAID/Indonesia higher education objectives by providing undergraduate training for at least five UNDIP students using STEM programs in place at UCSC, training on marine biotechnology for four undergraduate students, and curriculum development.

The exploitation of symbiotic bacteria as a source for novel secondary metabolites is considered to be in its infancy; however, the discovery rate of novel active metabolites from marine Gram-negative bacteria could surpass that of their terrestrial counterparts. Sponges represent an unusual niche for novel microbes, as they host hundreds of different bacterial groups and contain diverse symbionts. However, the marine environments in which they are found still remain largely unexplored, understudied, and underexploited. The urgent need for novel substances for the treatment of severe human diseases combined with the recognition that marine organisms provide a rich potential source of such substances support the intensive exploration of new substances from marine organisms. This project will use organisms and methods to overcome existing bottlenecks by using halotolerant Gram-negative bacteria, which can be grown in large scale in the laboratory and which are potent producers of bioactive compounds.

Summary of Recent Activities

Dr. Radjasa reports that he and his colleagues have published another paper recently in the Scopus-indexed journal PeerJ as a result of a PhD project supported by the PEER grant (see first citation below). The last quarter of 2019 also saw the completion of the six-month internships of six undergraduate students in Dr. Radjasa’s lab. In addition, the PEER team also purchased several new pieces of equipment, including an autoclave, refrigerator, pipettes, and an air filter device.

The third annual joint field sampling campaign on this project, which had been postponed and rescheduled for October 2019 in the waters off Raja Ampat, was once again postponed. It is currented set for February 1-6, 2020. Therefore, the goals for the remaining months of this project include completing the sampling campaign, preparing another manuscript for publication, and convening a national seminar for dissemination of the PEER project results and encouragement of linkages and idea sharing among stakeholders. Some additional laboratory equipment will be purchased, and the PI has also sent one of his research assistants on a three-month visit to the Genetics and Molecular Biotechnology Laboratory at the Bandung Institute of Technology ITB to learn new techniques on metagenomic analysis of the marine microbial community associated with marine invertebrates. A no-cost extension is being issued through May 31, 2020, to provide the necessary time to complete all project tasks.

Recent Publications

Kristiana, R., G. Bedoux, G. Pals, I.W. Mudianta, L. Taupin, C. Marty, M.A. Asagabaldan, D. Ayuningrum, A. Trianto, N. Bourgougnon, O.K. Radjasa, A. Sabdono, and M. Hanafi. 2020. Bioactivity of compounds secreted by symbiont bacteria of Nudibranchs from Indonesia. PeerJ 8:e8093 DOI: 10.7717/peerj.8093

Cristianawati, O., A. Sabdaningsih, L.E. Becking, M.M. Khoeri, H. Nuryadi, A. Sabdono, A. Trianto, and O.K. Radjasa. 2019. Biological activity of sponge-associated fungi from Karimunjawa Islands, Indonesia against pathogenic Streptococcus pneumonia. Biodiversitas 20(8): 2143-2150. DOI: 10.13057/biodiv/d200807

Trianto, A., O.K. Radjasa, A. Sabdono, S.I. Muchlissin, R. Afriyanto, Sulistiowati, S.K. Radjasa, P. Crews, and E. McCauley. 2019. Exploration culturable bacterial symbionts of sponges from Ternate Islands, Indonesia. Biodiversitas 20(3):776-782. DOI: 10/13057/biodiv/d200323.

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