Next generation sequencing reveals plants consumed by the vulnerable ebony langur (Trachypithecus auratus) in a fragmented mountain forest
##plugins.themes.bootstrap3.article.sidebar##
Issue
Section
Articles
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
##plugins.themes.bootstrap3.article.main##
PUGUH KARYANTO
♥
https://orcid.org/0000-0002-5581-2538
ADIFA RISA BAGASTA
IKE NURJUITA NAYASILANA
SHUKOR MD NOR
https://orcid.org/0000-0003-1579-1178
SRI SUCI UTAMI ATMOKO
https://orcid.org/0000-0001-5550-8344
ARI SUSILOWATI
https://orcid.org/0000-0002-0107-6870
SUNARTO
Abstract
Abstract. Karyanto P, Bagasta AR, Nayasilana IN, Nor SMD, Atmoko SSU, Susilowati A, Sunarto 2022. Next generation sequencing reveals plants consumed by the vulnerable ebony langur (Trachypithecus auratus) in a fragmented mountain forest. Biodiversitas 23: 4759-4769. Many mountain forests on Java Island have suffered from forest degradation, fragmentation, and alien species invasion that cause a significant change in vegetation structure. This changing floristic structure may affect the foraging substrate of the foliage eater ebony langur, Trachypithecus auratus. Hence, ascertaining the plants eaten by the langur may contribute significantly to informing important ecological data about its foraging adaptation and conservation. We analyzed six fecal samples of the langur from three forest sites in Mount Merbabu National Park, Indonesia. This research used the plant mini barcode to sequence the ribulose-biphosphate carboxylase gene (rbcl) in the mitochondrial DNA of the plants eaten by the langur using the Next Generation Sequencing. We compare the NGS results to floristic reference data from a vegetation survey preceding the fecal analysis. The NGS found 238 OTUs that belong to 32 taxa. Most of the langur’s diet belongs to the lower crop community. The study’s results suggest that the ebony langur’s dietary composition shows an adaptation to the new floristic composition. However, since the habitat is continuously degraded, the stakeholders must perform appropriate home-building-based habitat management practices to conserve this vulnerable species.
##plugins.themes.bootstrap3.article.details##
References
Ando, H., Setsuko, S., Horikoshi, K., Suzuki, H., & Umehara, S. (2013). Diet analysis by next-generation sequencing indicates the frequent consumption of introduced plants by the critically endangered red-headed wood pigeon ( Columba janthina nitens ) in oceanic island habitats. Ecology and Evolution, 3(12), 4057–4069. https://doi.org/10.1002/ece3.773
Ardiyaningrum, I., Budiastuti, M. T. S., & Komariah. (2021). Species composition and diversity of vegetation in dryland agricultural landscape. Biodiversitas, 22(1), 65–71. https://doi.org/10.13057/biodiv/d220109
Bell, K. L., Loeffler, V. M., & Brosi, B. J. (2017). An rbcL Reference Library to Aid in the Identification of Plant Species Mixtures by DNA Metabarcoding . Applications in Plant Sciences. https://doi.org/10.3732/apps.1600110
Bokulich, N. A., Subramanian, S., Faith, J. J., Gevers, D., Gordon, J. I., Knight, R., … Caporaso, J. G. (2013). Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods, 10(1), 57–59. https://doi.org/10.1038/nmeth.2276
Charles, H., & Dukes, J. S. (2007). 13 Impacts of Invasive Species on Ecosystem Services, (March 2017). https://doi.org/10.1007/978-3-540-36920-2
Cock, P. J. A., Fields, C. J., Goto, N., Heuer, M. L., & Rice, P. M. (2009). The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research, 38(6), 1767–1771. https://doi.org/10.1093/nar/gkp1137
Dewi, K. (2009). Forest Cover Change and Vulnerability of Gunung Merbabu National Park [tesis]. Master Program. Universitas Gadjah Mada.
Dunham, N. T. (2011). Coping with Forest Fragmentation: A Comparison of Colobus angolensis palliatus dietary diversity and behavioral plasticity in the East Sagara Forest, Tanzania. Honors Projects, Paper 36, 43.
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., & Knight, R. (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27(16), 2194–2200. https://doi.org/10.1093/bioinformatics/btr381
Erickson, D. L., Reed, E., Ramachandran, P., Bourg, N. A., McShea, W. J., & Ottesen, A. (2017). Reconstructing a herbivore’s diet using a novel rbcL DNA mini-barcode for plants. AoB PLANTS, 9(3). https://doi.org/10.1093/aobpla/plx015
Estrada, A., Garber, P. A., Mittermeier, R. A., Wich, S., Gouveia, S., Dobrovolski, R., … Setiawan, A. (2018). Primates in peril: The significance of Brazil, Madagascar, Indonesia and the Democratic Republic of the Congo for global primate conservation. PeerJ, 2018(6), 1–57. https://doi.org/10.7717/peerj.4869
Gerwing, T. G., Kim, J. H., Hamilton, D. J., Barbeau, M. A., & Addison, J. A. (2016). Diet reconstruction using next-generation sequencing increases the known ecosystem usage by a shorebird. Auk, 133(2), 168–177. https://doi.org/10.1642/AUK-15-176.1
Handayani, K. P., & Latifiana, K. (2019). Distribusi Spasial Surili Jawa (Presbytis comata) di Taman Nasional Gunung Merbabu. In D. Dwibadra, D. Citra Murniati, R. Rachmatika, I. P. G. Parlida Damayanto, N. Inayah, J. Giring Sukmawati, … A. Dyah Prawestri (Eds.), Riset Sebagai Fondasi Konservasi dan Pemanfaatan Tumbuhan dan Satwa Liar. Seminar Nasional Konservasi dan Pemanfaatan Tumbuhan dan Satwa Liar (pp. 118–125). Bogor: Pusat Penelitian Biologi LIPI. Retrieved from https://www.researchgate.net/publication/329642101%0ADistribusi
Hansen, K. D., Brenner, S. E., & Dudoit, S. (2010). Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Research, 38(12), 1–7. https://doi.org/10.1093/nar/gkq224
Isabirye-basuta, G. M., & Lwanga, J. S. (2008). Primate Populations and Their Interactions with Changing Habitats. Int J Primatol, 29(February), 35–48. https://doi.org/10.1007/s10764-008-9239-8
Jafari, S. M., Zarre, S., & Alavipanah, S. K. (2013). Woody species diversity and forest structure from lowland to montane forest in Hyrcanian forest ecoregion. Journal of Mountain Science, 10(4), 609–620. https://doi.org/10.1007/s11629-013-2652-2
Kool, K. M. (1992). Food Selection by the Silver Leaf Monkey, Trachypithecus auratus sondaicus, in Relation to Plant Chemistry. Oecologia, 90(4), 527–533. Retrieved from http://www.jstor.org/stable/4220009 Accessed:
Kool, K. M. (1993). The diet and feeding behavior of the silver leaf monkey (Trachypithecus auratus sondaicus) in Indonesia. International Journal of Primatology, 14(5), 667–700. https://doi.org/10.1007/BF02192186
Kress, W. J. (2017). Plant DNA barcodes?: Applications today and in the future. https://doi.org/10.1111/jse.12254
Kress, W. J., & Erickson, D. L. (2007). A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region. PLoS ONE, 2(6). https://doi.org/10.1371/journal.pone.0000508
Kumarathunge, D. P., Thattil, R. O., & Nissanka, S. P. (2011). Evaluation of the plotless sampling method to estimate aboveground biomass and other stand parameters in tropical rain forests. Applied Ecology and Environmental Research, 9(4), 425–431. https://doi.org/10.15666/aeer/0904_425431
Lavigne, F., & Gunnell, Y. (2006). Land cover change and abrupt environmental impacts on Javan volcanoes, Indonesia: A long-term perspective on recent events. Regional Environmental Change, 6(1–2), 86–100. https://doi.org/10.1007/s10113-005-0009-2
Linders, T. E. W., Schaffner, U., Eschen, R., Abebe, A., Choge, S. K., Nigatu, L., … Allan, E. (2019). Direct and indirect effects of invasive species: Biodiversity loss is a major mechanism by which an invasive tree affects ecosystem functioning. Journal of Ecology. https://doi.org/10.1111/1365-2745.13268
Mago?, T., & Salzberg, S. L. (2011). FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 27(21), 2957–2963. https://doi.org/10.1093/bioinformatics/btr507
Nijman, V. (2000). Geographic distribution of ebony leaf monkey Trachypithecus auratus (E. Geoffroy Saint-Hilaire, 1812) (Mammalia: Primates: Cercopithecidae). Contribution to Zoology, 69(3), 157–177. https://doi.org/DOI: 10.1163/18759866-06903002
Nijman, V. (2013). Distribution and Ecology of the Most Tropical of the High-Elevation Montane Colobines: The Ebony Langur on Java. In N. Grow, S. Gursky-Doyen, & A. Krzton (Eds.), High Altitude Primates (pp. 115–132). New York: Springer US. https://doi.org/10.1007/978-1-4614-8175-1
Nsubuga, A. M., Robbins, M. M., Roeder, A. D., Morin, P. A., Boesch, C., & Vigilant, L. (2004). Factors affecting the amount of genomic DNA extracted from ape faeces and the identification of an improved sample storage method. Molecular Ecology, 13(7), 2089–2094. https://doi.org/10.1111/j.1365-294X.2004.02207.x
Padmanaba, M., Tomlinson, K. W., Hughes, A. C., & Corlett, R. T. (2017). Alien plant invasions of protected areas in Java, Indonesia. Scientific Reports, 7(1), 1–11. https://doi.org/10.1038/s41598-017-09768-z
Pompanon, F., Deagle, B. E., Symondson, W. O. C., Brown, D. S., Jarman, S. N., & Taberlet, P. (2012). Who is eating what: Diet assessment using next generation sequencing. Molecular Ecology, 21(8), 1931–1950. https://doi.org/10.1111/j.1365-294X.2011.05403.x
Prasetyo, L. B., Kartodihardjo, H., Adiwibowo, S., Okarda, B., & Setiawan, Y. (2009). Spatial model approach on deforestation of Java Island, Indonesia. Journal of Integrated Field Science, 6(June 2014), 37–44.
Quéméré, E., Hibert, F., Miquel, C., Lhuillier, E., Rasolondraibe, E., Champeau, J., … Chikhi, L. (2013). A DNA Metabarcoding Study of a Primate Dietary Diversity and Plasticity across Its Entire Fragmented Range. PLoS ONE, 8(3). https://doi.org/10.1371/journal.pone.0058971
Rivera, A., & Calmé, S. (2005). Forest Fragmentation and Its Effects on the Feeding Ecology of Black Howlers (Alouatta pigra) from the Calakmul Area in Mexico. In A. Estrada, P. A. Garber, M. S. M. Pavelka, & L. Luecke (Eds.), New Perspectives in the Study of Mesoamerican Primates (pp. 189–213). New York: Springer. https://doi.org/10.1007/0-387-25872-8_9
Rytkönen, S., Vesterinen, E. J., Westerduin, C., Leviäkangas, T., Vatka, E., Mutanen, M., … Orell, M. (2019). From feces to data: A metabarcoding method for analyzing consumed and available prey in a bird-insect food web. Ecology and Evolution, 9(1), 631–639. https://doi.org/10.1002/ece3.4787
Sagar, R., Raghubanshi, A. S., & Singh, J. S. (2008). Comparison of community composition and species diversity of understorey and overstorey tree species in a dry tropical forest of northern India. Journal of Environmental Management, 88(4), 1037–1046. https://doi.org/10.1016/j.jenvman.2007.05.013
Silva, V. Da, Silva, V. L. da, Silva, V. Da, Costa, D. D. A., Silva, F. D. A. da, Silva, G. M. B. da, & Christoffersen, M. L. (2018). Abundance of Trees Used As Food By Primates in Fragments of Atlantic Forest. Environmental Smoke, 1(1), 20–41. https://doi.org/10.32435/envsmoke.20181120-41
Smiet, A. C. (1992). Forest Ecology On Java: Human Impact And Vegetation Of Montane Forest. Journal of Tropical Ecology, 8(2), 129–152. https://doi.org/10.1017/S026646740000626X
Tsuji, Y., Mitani, M., Widayati, K. A., Suryobroto, B., & Watanabe, K. (2019). Dietary habits of wild Javan lutungs (Trachypithecus auratus) in a secondary-plantation mixed forest: Effects of vegetation composition and phenology. Mammalian Biology, 98, 80–90. https://doi.org/10.1016/j.mambio.2019.08.001
Tsujino, R., Yumoto, T., Kitamura, S., Djamaluddin, I., & Darnaedi, D. (2016). History of forest loss and degradation in Indonesia. Land Use Policy, 57, 335–347. https://doi.org/10.1016/j.landusepol.2016.05.034
Zhong, W., Tan, Z., Wang, B., & Yan, H. (2019). Next-generation sequencing analysis of Pardosa pseudoannulata’s diet composition in different habitats. Saudi Journal of Biological Sciences, 26(1), 165–172. https://doi.org/10.1016/j.sjbs.2018.08.004
Most read articles by the same author(s)
- DIAN SAGITA FITRI, ARTINI PANGASTUTI, ARI SUSILOWATI, SUTARNO SUTARNO, Endophytic bacteria producing antibacterial against methicillinresistant Staphylococcus aureus (MRSA) in seagrass from Rote Ndao, East Nusa Tenggara, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 18 No. 2 (2017)
- FATIHA RISTYA AZ-ZAHRA, NERIZA LARAS WIDYA SARI, RAIHANI SAPUTRY, GILANG DWI NUGROHO, TEGUH PRIBADI, SUNARTO, AHMAD DWI SETYAWAN, Review: Traditional knowledge of the Dayak Tribes (Borneo) in the use of medicinal plants , Biodiversitas Journal of Biological Diversity: Vol. 22 No. 10 (2021)
- FARIDA HIKMAWATI, ARI SUSILOWATI, RATNA SETYANINGSIH, Colony morphology and molecular identification of Vibrio spp. on green mussels (Perna viridis) in Yogyakarta, Indonesia tourism beach areas , Biodiversitas Journal of Biological Diversity: Vol. 20 No. 10 (2019)
- AHMAD DWI SETYAWAN, INDROWURYATNO INDROWURYATNO, WIRYANTO WIRYANTO, KUSUMO WINARNO, ARI SUSILOWATI, Mangrove plants in coastal area of Central Java: 2. Floristic composition and vegetation structure , Biodiversitas Journal of Biological Diversity: Vol. 6 No. 3 (2005)
- ARI SUSILOWATI, SHANTI LISTYAWATI, Source of contaminant microorganisms in in vitro culture at Sub lab. Biology, Central Laboratory of Mathematics and Sciences, Sebelas Maret University , Biodiversitas Journal of Biological Diversity: Vol. 2 No. 1 (2001)
- AHMAD DWI SETYAWAN, INDROWURYATNO INDROWURYATNO, WIRYANTO WIRYANTO, KUSUMO WINARNO, ARI SUSILOWATI, Mangrove plants in coastal area of Central Java: 1. Species diversity , Biodiversitas Journal of Biological Diversity: Vol. 6 No. 2 (2005)
- ARTINI PANGASTUTI, RIZAL KHOIRUN ALFISAH, NUR IFFAH ISTIANA, SITI LUSI ARUM SARI, RATNA SETYANINGSIH, ARI SUSILOWATI, TJAHJADI PURWOKO, Metagenomic analysis of microbial community in over-fermented tempeh , Biodiversitas Journal of Biological Diversity: Vol. 20 No. 4 (2019)
- AHMAD DWI SETYAWAN, JATNA SUPRIATNA, NISYAWATI, ILYAS NURSAMSI, SUTARNO, SUGIYARTO, SUNARTO, PRAKASH PRADAN, SUGENG BUDIHARTA, ARI PITOYO, SAPTA SUHARDONO, PRABANG SETYONO, MUHAMMAD INDRAWAN, Predicting potential impacts of climate change on the geographical distribution of mountainous selaginellas in Java, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 21 No. 10 (2020)
- SITI LUSI ARUM SARI, ARTINI PANGASTUTI, ARI SUSILOWATI, TJAHJADI PURWOKO, EDWI MAHAJOENO, WAHYU HIDAYAT, IKOW MARDHENA, DEWI KURNIAWATI, ROBIAH ANITASARI, Cellulolytic and hemicellulolytic bacteria from the gut of Oryctes rhinoceros larvae , Biodiversitas Journal of Biological Diversity: Vol. 17 No. 1 (2016)
- SYAHIK NUR BANI, DYAH PERWITASARI-FARAJALLAH, SRI SUCI UTAMI ATMOKO, JAMARTIN SIHITE, Adaptation behavior of Bornean Orangutan (Pongo pygmaeus morio) reintroduction in Kehje Sewen Forest, East Kalimantan, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 19 No. 3 (2018)