Category Archives: Indonesia

Voucher specimens of IndoBioSys project repatriated to the Museum Zoologicum Bogoriense

In April and May 2016, the first two batches of vouchers, about 2,000 mounted and labelled specimens of insects, were repatriated to the collection of the Museum Zoologicum Bogoriense, Research Center for Biology – LIPI, in Cibinong, Indonesia. The specimens were processed through the DNA barcoding pipeline at the Zoologische Staatssammlung München (ZSM) as part of the IndoBioSys project – Indonesian Biodiversity Discovery System.

The project aims at developing new approaches to discover and describe Indonesian biodiversity. IndiBioSys is a G-to-G (government to government) initiative between Germany and Indonesia, funded by the German Federal Ministry of Education and Research (BMBF) and the Indonesian State Ministry of Research and Technology (RISTEK). The ZSM is, in cooperation with the Museum Zoologicum Bogoriense, establishing a novel high-throughput biodiversity discovery pipeline that is based on DNA barcoding as an efficient mean to assess the biodiversity of a region that is among the world’s top biodiversity hotspots.

DNA barcoding is a molecular tool for the fast and reliable identification of biological specimens and for the discovery of unknown species. Specimens of unknown identity are assigned a unique identifier based on DNA sequence data to make the species recognisable without the need for the immediate formal taxonomic treatment that is usually laborious and time-consuming. Traditional taxonomic practices have often been a major obstacle for the fast and efficient discovery and characterization of unknown biodiversity.

The returned voucher specimens will be permanently deposited in the MZB as Indonesia’s national zoological repository. Together with the data that are associated with the specimens (collecting data, sequences, photographs, biological data, etc.), the barcoded specimens represent a valuable source for research projects in the future.

ZSM runs DNA barcoding training at the MZB in Cibinong, West Java

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Staff members of the MZB participating in a training course on DNA barcoding.

The ZSM is currently running a training course at the Museum Zoologicum Bogoriense (MZB), Research Center for Biology – LIPI in Cibinong, Indonesia. The IndoBioSys coordinator at the ZSM, Bruno Cancian, is instructing Indonesian project partners to process voucher specimens according to a standardised protocol that was developed by the Canadian Centre for DNA Barcoding (CCDB) in Guelph, Canada. The procedure is part of a high-throughput workflow that was established at the ZSM as part of several large-scale DNA barcoding projects, including the Barcoding Fauna Bavarica and the German Barcode of Life projects. The optimised workflow enabled the ZSM to process nearly 200.000 specimens since the first barcoding projects commenced at the ZSM about 10 years ago.

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Participant of the training course processing specimens obtained from Malaise trap samples.

The preparation of voucher specimens for DNA barcoding involves image capture, recording of collecting data, sampling (leg picking), and transfer of samples to PCR plates that are subsequently processed at the CCDB. The data are maintained and managed using the Barcode of Life Database System as database management system that allows Indonesian and German project partners to access and analyse the data as soon as they are available, anywhere and at any time.

Specimens for barcoding were obtained during an expedition of Indonesian, German, and British specialists. Most of the material, primarily insects that comprise the largest number unknown organisms in the Indonesian fauna, was collected using Malaise traps. These traps are the most efficient method for obtaining a lot of insects in a very short time frame.

IndoBioSys project is a joint project of the ZSM in Munich and headed by the Museum für Naturkunde in Berlin on the German side, and the MZB/LIPI on the Indonesian side. The project is funded by the Federal Ministry of Education and Research and the Indonesian State Ministry of Research and Technology. It aims at establishing a novel high-throughput biodiversity discovery pipeline that is based on DNA barcoding as efficient means to assess the biodiversity of a region that is among the world’s top biodiversity hotspots.

DNA barcoding of Indonesian biodiversity – the IndoBioSys project

IndoBioSys – Indonesian Biodiversity Discovery System – aims at developing new approaches to discover and describe Indonesian biodiversity. The ZSM is, in cooperation with the Museum Zoologicum Bogoriense, Research Center for Biology – LIPI in Cibinong, Indonesia, establishing a novel high-throughput biodiversity discovery pipeline that is based on DNA barcoding as efficient means to assess the biodiversity of region that is among the world’s top biodiversity hotspots.

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Malaise trap for collecting insects set up in the study area

The first field expedition to the study area, the Halimun-Salak National Park in West Java, was conducted during September and October 2015. A team of specialists from Germany, Austria, the UK, and their project partners from the Museum Zoologicum Bogoriense, Research Center for Biology – LIPI (MZB) collected their taxa of interest using a range of different standardised methods, including Malaise traps, net sweeping, and light trapping.

Novie Safita from Universitas Andalas in Padang, Sumatra, taking images of voucher specimens with a Keyence VHX-5000 digital microstope at the ZSM.

The samples that were obtained during the field trip are currently being processed at the MZB in Cibinong and the ZSM in Munich. Since November 2015, nearly 4,000 samples have been processed. The first results reflect the high quality of the samples and are most promising for establishing an efficient and standardized system for species identification of the poorly known Indonesian fauna.

The majority of specimens that are present in the Malaise trap and sweep net samples belong to groups of organisms that are known to be very diverse in tropical countries but very little known yet. It is estimated that well over 90% of the species discovered as part of the project will be new to science, in particular Hymenoptera, Diptra, and Coleoptera. All barcoding voucher specimens are deposited at the MZB in Cibinong, Indonesia.

IndoBioSys oucher specimens processed for DNA barcoding (from top left to bottom right (Hymenoptera: Braconidae, Lepidoptera: Geometridae: Mnesiloba, Coleoptera, Lepidoptera: Geometridae: Polynesia, Hymenoptera: Apoidea, Hymenoptera: Chrysididae, Hymenoptera: Vespidae: Eumeninae, Lepidoptera: Geometridae: Tristeirometra, Coleoptera).

IndoBioSys voucher specimens processed for DNA barcoding (to row from left to right : Hymenoptera: Braconidae, Lepidoptera: Geometridae: Mnesiloba, Coleoptera; middle row: Lepidoptera: Geometridae: Polynesia, Hymenoptera: Apoidea, Hymenoptera: Chrysididae; bottom row: Hymenoptera: Vespidae: Eumeninae, Lepidoptera: Geometridae: Tristeirometra, Coleoptera).

Stefan Schmidt / ZSM
Olga Schmidt / ZSM

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Contact
Dr. Bruno Cancian, coordinator
indobiosys-zsm@zsm.mwn.de

Towards an Indonesian-German Biodiversity Network

Researchers from the Zoologische Staatssammlung visited Indonesia in an effort to establish collaborative projects with universities in Sumatra and Java, and in the near future, the project collaboration will be expanded more broadly with the Indonesian Institute of Sciences (LIPI).

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Collecting insects in Harau Valley, West Sumatra.

During two weeks each at the Andalas University in Padang (West Sumatra) and Brawijaya University in Malang (East Java), Stefan and Olga Schmidt, Michael Balke, and PhD student Emmanuel Toussaint conducted courses to implement the module “DNA Barcoding of Arthropods” as part of the “Indonesian-German Network – Training of Trainers and Research Cooperation” (IGN-TTRC).

Durian

A snack after collecting in Harau Valley. The taste of Durian – a mixture of rotten meat and vanilla – is not everybody’s cup of tea.

IGN-TTRC is a consortium to improve teaching, training and research collaborations within Indonesia and between Indonesia and Germany, funded by the German Academic Exchange Service (DAAD). The objective of the program is to give an overview of the role of molecular biology methods in biodiversity research. Topics covered in the lectures include general entomology and molecular systematics, but also practical exercises in the field (collecting aquatic insects, Hymenoptera, and Lepidoptera), insect preparation, and molecular work including DNA extraction, PCR, sequencing, sequence analysis, species identification using the Barcode of Life Database (Bold), and using DNA barcoding for MBA (molecular biodiversity assessment).

The participants of the courses came from over a dozen different universities across Indonesia, from Sumatra, Java, Kalimantan, and Sulawesi. Course subjects will be used to develop a joint curriculum leading to joint MSc programs and to establish conditions to facilitate the acceptance of Indonesian students into MSc and PhD programs at German Universities. Besides the training component of the courses, the aim of IGN-TTRC is to establish research cooperations between Indonesian and German institutions with joint projects and exchange of students.

Collecting

Who will be the first to jump into the rice paddy for collecting water beetles?

Before the barcode there is lab work.

Before the barcode there is lab work.

The study objects for the courses were selected according to the research areas of the German trainers and included primarily aquatic insects , microhymenoptera, and geometrid moths. Collecting methods were as diverse as the insects of interest and included sweep netting, yellow pan traps, kitchen strainers for aquatic insects, and collecting at a light sheet at night.

Indonesia’s biodiversity is unique in the world. Indonesia is a country of mega-diversity, rivalled only by Brazil, Colombia, and Zaire. The 17.000 islands that comprise Indonesia occupy only 1.3% of the world’s land mass, but the country is home of about 12% of the mammals and 17% of the birds of the world. Estimates of the species richness of insects are difficult, but it is probably safe to assume that in little known groups like microhymenoptera, only a tiny fraction of the species have been discovered.

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Tropical rainforest in West Sumatra, home of a myriad of new species awaiting discovery.

ZSM Forscher auf Trainigsmission in Indonesien

Insektenforscher der ZSM sind derzeit in Indonesien unterwegs, und zwar als Trainer in Sachen Biodiversitätsforschung an den Universitäten in Padang (West Sumatra) und Malang (Ost Java). Der Aufenthalt wird vom DAAD gefördert. Dabei werden indonesische Universitätsdozenten in Fragen rund ums DNA Barcoding und klassischer Entomologie unterrichtet – eine Woche lang. In einer zweiten Woche geben sie ihr Wissen dann jeweils an eine Gruppe von Studenten weiter. Aus diesem Projekt sind bereits Kooperationen zwischen der ZSM und indonesischen Partnern erwachsen, der erste Gegenbesuch ist bereits im September 2012 geplant!

Dr Nia Kurniawan (UB Malang) gibt Studenten eine Einführung in Methoden der aquatischen Entomologie, ZSM Gastforscher Emmanuel Toussaint lauscht gespannt.