DeepDyve requires Javascript to function. Please enable Javascript on your browser to continue.
A preliminary analysis of the diet composition of overwintering Bean geese (Anser fabalis) and greater white-fronted geese (A. albifrons) in Korea using PCR on fecal samples A preliminary analysis of the diet composition of overwintering Bean geese (Anser fabalis) and...
Kim, Min Kyung; Lee, Sang-im; Kim, Baek-Jun; Lee, Sang Don
2017-03-04 00:00:00
ECOLOGY, POPULATION BIOLOGY & ANIMAL BEHAVIOR ANIMAL CELLS AND SYSTEMS, 2017 VOL. 21, NO. 2, 141–145 http://dx.doi.org/10.1080/19768354.2017.1308437 A preliminary analysis of the diet composition of overwintering Bean geese (Anser fabalis) and greater white-fronted geese (A. albifrons) in Korea using PCR on fecal samples a b c a Min Kyung Kim , Sang-im Lee , Baek-Jun Kim and Sang Don Lee a b Department of Environmental Science and Engineering, College of Engineering, Ewha Womans University, Seoul, Korea; School of Undergraduate Studies, Daegu-Gyeongbuk Institute of Science and Technology, Daegu, Korea; National Institute of Ecology, Seocheon, South Korea ABSTRACT ARTICLE HISTORY Received 23 October 2016 Bean geese (Anser fabalis) and Greater white-fronted geese (Anser albifrons) are the dominant Revised 2 February 2017 wintering waterfowl in South Korea. Although they are commonly observed in estuaries and rice Accepted 2 March 2017 fields during the winter, the diet composition of the geese during the winter has rarely been studied. In this study, we provide the results from preliminary analyses on the diet of these two KEYWORDS geese species overwintering in Daebu Island of South Korea. We used a total of 13 fecal samples Diet; feces; Anser fabalis; from Bean geese (n = 4) and Greater white-fronted geese (n = 9), and performed a BLAST search Anser albifrons; South Korea for the sequences obtained from 87 clones (n = 36 for Bean geese and n = 51 for Greater white- fronted geese). The diet of Bean geese consisted of five families of plants: Caryophyllaceae (75.0%), Poaceae (13.9%), Asteraceae (5.5%), Polygonaceae (2.8%) and Cucurbitacea (2.8%). On the other hand, the diet of Greater white-fronted geese consisted of 6 families of plants: Poaceae (74.5%), Caryophyllaceae (9.8%), Solanacea (5.9%), Portulacaceae (3.9%), Lamiaceae (3.9%) and Brassicaceae (2.0%). We found that plants of the rice family (Poaceae) are important in the diet of wintering geese, especially for Greater white-fronted geese. This knowledge can be used to establish conservation strategies of the geese overwintering in South Korea. Introduction Endangered species level II in Korea; Rho et al. 2010), their ecology has rarely been studied in South Korea. In Most species of geese migrate long distances between particular, understanding the diet composition is their breeding sites and wintering sites. Among them, pivotal in establishing conservation strategies (Marrero the Bean goose (Anser fabalis) and Greater white- et al. 2004; Valentini et al. 2009) but the diet composition fronted goose (Anser albifrons) are the most common of the geese during their wintering in South Korea has visitors in South Korea (Park & Won 1993). The breeding not yet been identified, except some descriptions on populations in the Asian arctic region is 140,000 for the their consumption of ‘waste rice (Stafford et al. 2006)’ Bean goose and 165,000–235,000 for the Greater (Yoo et al. 2008). white-fronted goose (Syroechkovskiy 2006). Among Non-invasive samples such as feces, hair and feather them, more than 50,000 Bean geese and 69,000 are useful for species, sex and diet identification of Greater white-fronted geese overwinter in South Korea endangered and/or elusive species (Sacchi et al. 2004; (Ministry of Environment 2009, 2010, 2011, 2012, 2013). Horvath et al. 2005; Waits & Paetkau 2005; Deagle et al. For long-distance migratory birds such as the Bean 2007; Kim et al. 2011). For geese, most studies generally goose and Greater white-fronted goose, it is important use invasive samples, such as blood and tissue samples to build up their nutritional status before migrating (Quinn et al. 1991; Huang et al. 2003), and only a few back to their breeding grounds. In addition, the studies used non-invasive samples, such as feathers feeding status during the winter influences the pro- (Kim et al. 2012; Kleven et al. 2016). Several non-invasive ductivity of the migratory birds in the subsequent breed- methods have been used for diet analysis of herbivores, ing season (Robb et al. 2008). In spite of the recent including: (i) microscopical examination of plant cuticle attention to the conservational status of these geese fragments in fecal samples, (ii) chemical analysis of the (especially the Bean goose, which was designated as CONTACT Sang Don Lee lsd@ewha.ac.kr Department of Environmental Science and Engineering, College of Engineering, Ewha Womans University, Seoul 120-750, Korea © 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 142 M. K. KIM ET AL. natural alkanes of plant cuticular wax, (iii) near-infrared of the representative wintering sites of the geese in reflectance spectroscopy, and (iv) detection of plant South Korea. Thirteen fecal samples of geese were col- DNA using PCR (Deagle et al. 2007; Valentini et al. lected in January 2010 in Daebu Island, Korea. Daebu 2009). The methods for plant DNA detection are still Island includes a large reclaimed area that is recently being developed (Oehm et al. 2011). However, diet serving as a main habitat for hundreds of bird species analysis of the geese using non-invasive samples has (Ministry of Environment 2004). Fecal samples of geese not been conducted except one study on the Barnacle were frozen at −20°C right after the collection until used. goose (Branta leucopsis) by Stech et al. (2011). Consider- ing that geese are a representative group of migrating birds and their migration ecology is studied globally, Molecular methods the rarity of ecological studies using non-invasive Genomic DNA was extracted from 13 fecal samples (up samples is surprising. In this study, we conducted PCR- to 200 mg fecal samples) following Gerloff et al. (1995). based analysis of the diet composition of Bean geese Since the two geese species usually formed a mixed- and Greater white-fronted geese using fecal samples col- species wintering flock, it was difficult to tell which lected in their wintering grounds in South Korea. fecal sample belonged to which species. Therefore, we first conducted species identification for the fecal Materials and methods samples using the method described by Kim et al. (2012). Study area and sampling site For the diet analysis, we used a pair of primers, rbcL The Bean goose and Greater white-fronted goose over- Z1aF and hp2R, to amplify the gene of large subunit of winter near the West and South coast region of Korea the ribulose-1,5-bisphosphate carboxylase (rbcL) from mostly in wetlands, such as reclaimed land or marsh feces (following Kim et al. 2011). Genomic DNA was (Kim et al. 2016). We selected Daebu Island (126° extracted from the fecal samples (100 mg out of the pre- ′ ′′ ′ ′′ ′ ′′ ′ ′′ 34 30 –126°39 0 E, 37°15 0 –37°16 30 N; Figure 1)on pared fecal samples) following Gerloff et al. (1995). The the West Coast as the collection site because it is one chloroplast rbcL gene has been widely used to analyze Figure 1. Location of the collection site. Location (a) and satellite map of Daebu Island (b). ANIMAL CELLS AND SYSTEMS 143 the diet of herbivorous species (reviewed in Valentini Table 1. Plants in the diets of the bean goose and greater white- fronted goose in Daebu Island. et al. 2009). The PCRs were carried out in a 25 μl reaction Greater white- volume containing 2 μl of DNA template, 2 mM of MgCl , Bean goose fronted goose 1X PCR buffer (iNtRON Inc., South Korea), 0.2 mM of each No. of %of No. of %of dNTP, 0.1 μM of each primer, 2.5 μg of BSA (Promega Inc., Order Family clones clones clones clones a a USA) and 1U of i-Star Taq polymerase (iNtRON Inc., South Poales Poaceae 5 13.9 38 74.5 Caryophyllales Caryophyllaceae 27 75.0 5 9.8 Korea). The PCR amplifications were performed using Polygonaceae 1 2.8 PTC-100 PCR Thermal Cycler (MJ Research Inc., USA) Portulacaceae 2 3.9 Brassicales Brassicaceae 1 2.0 with the following conditions: initial denaturation for 3 Solanales Solanacea 3 5.9 min at 94°C, followed by 50 cycles of amplification (94° Lamiales Lamiaceae 2 3.9 Cucurbitales Cucurbitacea 1 2.8 C for 45 s, 55°C for 30 s and 72°C for 45 s) with a final Asterales Asteraceae 2 5.5 extension for 3 min at 72°C. After purifying the PCR pro- Total 36 100 51 100 TM ducts on 3% agarose gel using Zymoclean Gel DNA Sequences from one clone could also be assigned to a genus that does not belong to this taxonomic group. Refer to Table 2 for the details. Recovery Kit (Zymo Research Corp., Japan), cloning was carried out with RBC T&A Cloning Kit under the manufac- turer’s instructions (Real Biotech Corp., Taiwan). For were identified (Table 1). Poaceae (74.5%) was the most colony sequencing, we conducted PCRs with universal dominant diet plant, followed by Caryophyllaceae (9.8%), M13F and M13R primers using the samples taken from Solanacea (5.9%), Portulacaceae (3.9%), Lamiaceae (3.9%) colonies. After colony PCR, only the forward primer, and Brassicaceae (2.0%) (Table 1). The diet composition M13F, was used for sequencing. All PCR products were estimated in this study at the family level was different directly sequenced using the ABI PRISM 3700 DNA between the two geese species (χ = 139.98, P < .001). sequencer (Applied Biosystems Inc., USA). Many genera that recorded the highest scores from The length of the partial rbcL PCR product was 202 bp the BLAST search were also found in the catalogue of excluding the primer binding regions. The sequences the vascular plants previously surveyed in the study were aligned with AlignIR program version 2.1 (LI-COR site (Table 2). In addition, two genera for crops (such as Inc., USA). These sequences were compared with rbcL rice Oryza or daikon Raphanus) were identified from sequences that are published in GenBank by means of the list of genera obtained from BLAST search. This nucleotide BLAST search, and the order and family of suggests that our molecular method can be used as a the closest matches were recorded. Statistical compari- valid method for estimation of the diet composition of son of the two geese species in their diet composition the geese from non-invasive samples. (at the family level) was conducted with chi-square tests. A drawback of using BLAST search for estimating the In order to provide more detailed understanding of the diet composition is that some ambiguities can arise. In diet composition, we presented the list of genera showing our analyses, there were two ambiguous cases: The highest Max scores and identity values recognized by rbcL sequence from one clone showed the highest BLAST search. We additionally provided the identity of matching scores (100%) with two genera (Phragmites the plant species by comparing the list of genera recorded and Coelachne) from Poaceae and Hydrilla from Hydro- from BLAST search with the species list of vascular plants charitaceae. Plant species belonging to these three surveyed in Daebu Island (Lim et al. 2014). genera were found in the vascular plant list reported in Daebu Island. We could frequently observe that both Results and discussion geese species feed the roots of plants belonging to Phragmite and Coelachne. In contrast, we have not Among 13 fecal samples, four were identified to be from observed that the geese forage plants belonging to the Bean goose. From the 4 samples, we obtained a total Hydrilla (Kim BJ, Pers. Obs). Based on this observation, of 36 clones containing plant rbcL genes. From the 36 we think the likelihood that Hydrilla from Hydrocharita- clones, a total of 4 orders and 5 families of plants were ceae is present in the diet of the geese is low. Similarly, recognized (Table 1). Caryophyllaceae (75.0%) was the Persea from Lauraceae was recognized together with a most dominant diet plant, followed by Poaceae genera (Youngia) from Asteraceae for the rbcL sequence (13.9%), Asteraceae (5.5%), Polygonaceae (2.8%) and from the other clone with 98% identity values. In the vas- Cucurbitacea (2.8%) (Table 1). cular plant list recorded from the study site, one plant The rest of fecal samples (n = 9) were identified to be species belonging to Youngia is present but no species from the Great white-fronted goose. From these samples, from Persea is present. Thus, we think that it is plausible a total of 51 clones with plant rbcL genes were successfully that Persea is not present in the diet of the geese. Such sequenced and a total of 5 orders and 6 families of plants 144 M. K. KIM ET AL. Table 2. Plants from the feces of the Greater white-fronted geese and Bean geese. The genera that were present in the catalogue of vascular plants surveyed at the study site (Lim et al. 2014) are marked with bold; the genera that were likely to be present but not listed in the catalogue (such as crops) are underlined. Order Family List of genera with the highest score from BLAST search Bean goose Poales Poaceae Aira, Arundinella, Castellia, Chikusichloa, Coelachne, Deschampsia, Festuca, Helictochloa, Helictotrichon, Lamarckia, Lolium, Oryza, Phragmites, Rhynchoryza, Sesleria, Vulpia Caryophyllales Caryophyllaceae Cerastium, Myosoton, Silene, Spergularia, Stellaria, Viscaria Polygonaceae Bistorta, Persicaria, Polygonum Cucurbitales Cucurbitaceae Trichosanthes Asterales Asteraceae Aster, Youngia Alismatales Hydrocharitaceae Hydrilla (recognized with Poaceae from the same clone) Laurales Lauraceae Persea (recognized with Asteraceae from the same clone) Greater white- Poales Poaceae Ancistrachne, Arthrostylidium, Arundinella, Aulonemia, Bambusa, Borinda, Buergersiochloa, fronted goose Chikusichloa, Coelachne, Dendrocalamus, Dichanthelium, Echinochloa, Elytrophorus, Eragrostis, Eriochloa, Greslania, Leersia, Loudetia, Melocanna, Neololeba, Oryza, Panicum, Phalaris, Phragmites, Rhipidocladum, Rhynchoryza, Schizostachyum, Scutachne, Thyrsostachys, Yakirra, Zizania Caryophyllales Caryophyllaceae Cerastium, Myosoton, Silene, Spergularia, Stellaria Portulacaceae Portulaca Brassicales Brassicaceae Raphanus Solanales Solanacea Brugmansia, Capsicum, Datura, Dunalia, Iochroma, Saracha, Solanum, Vassobia, Withania Lamiales Lamiaceae Isodon Alismatales Hydrocharitaceae Hydrilla (recognized with Poaceae from the same clone) ambiguities can be circumvented by amplifying longer increase in agricultural lands due to the reclamation sequences and/or using less conservative genetic project on the West Coast of Korea (Kim et al. 2016). marker than rbcL in future studies. Even though our study was a preliminary one invol- Our results show that, even though the Bean goose ving small number of samples, it shows the usefulness and Greater white-fronted goose form mixed-species of non-invasive samples for diet analysis of herbivores wintering flocks and co-occur in many wintering and promotes further molecular studies of similar grounds in South Korea, the diet composition of the scopes. Our preliminary results can also be used in two species differs. Although their ecological niches are collecting information necessary for establishment of often assumed to be identical, detailed use of habitats conservation strategies for geese populations overwin- between the two species differed (Kim et al. 2016). Pre- tering in East Asia where the rice fields are abundant. sumably, Greater white-fronted geese prefer rice In the future, a new advanced technique such as Next paddies, whereas Bean geese use wetlands. As we used Generation Sequencing (NGS) of plant DNAs from fecal a small number of fecal samples and clones in the samples, would be applicable for the diet analysis as an present study, a larger-scale study has to be conducted alternative of cloning technique. in order to fully ascertain the difference of diet compo- sition of these two geese species. Acknowledgements In winter, the Bean goose and Greater white-fronted The authors thank Dr George A. Lozano for providing useful goose mostly feed on crops, such as rice left on the rice comments. fields (Pers. Obs; Yoo et al. 2008). In our results, the main component of the diet of the Greater white-fronted goose was Poaceae which includes rice. For the Bean Disclosure statement goose, the family Poaceae constituted the second major No potential conflict of interest was reported by the authors. item in their diet. Considering that we had small samples for the Bean goose and the main diet of a related species, Lesser white-fronted goose Funding (A. erythropus) wintering in the Evros Delta, Greece, was The authors wish to thank NRF [2015M3C8A6A06012735, 2009- rice (Karmiris et al. 2014), it is plausible that many geese 0083527, 2013-005769] for financial support. species heavily rely on the waste rice in wintering grounds. The importance of rice in conservation of diverse bird species, especially waterbirds, is already References recognized by many studies (e.g. Stafford et al. 2006;Staf- Deagle BE, Gales NJ, Evans K, Jarman SN, Robinson S, Trebilco R, ford et al. 2010). Populations of the Greater white-fronted Hindell MA. 2007. Studying seabird diet through genetic goose wintering in Korea have increased in mid-2000s analysis of faeces: a case study on macaroni penguins (Syroechkovskiy 2006), and this may be related to the (Eudyptes chrysolophus). PLoS ONE. 2:e831. ANIMAL CELLS AND SYSTEMS 145 Gerloff U, Schlötterer C, Rassmann K, Rambold I, Hohmann G, Ministry of Environment. 2012. Winter migratory bird census (in Fruth B, Tautz D. 1995. Amplification of hypervariable Korean). Incheon: ROK: Ministry of Environment. simple sequence repeats (microsatellites) from excremental Ministry of Environment. 2013. Winter migratory bird census (in DNA of wild living bonobos (Pan paniscus). Mol Ecol. Korean). Incheon: ROK: Ministry of Environment. 4:515–518. Oehm J, Juen A, Nagiller K, Neuhauser S, Traugott M. 2011. Horváth MB, Martínez-Cruz B, Negro JJ, Kalmár L, Godoy JA. Molecular scatology: how to improve prey DNA detection 2005. An overlooked DNA source for non-invasive genetic success in avian faeces? Mol Ecol Res. 11:620–628. analysis in birds. J Avian Biol. 36:84–88. Park JY, Won PO. 1993. Wintering ecology of Bean goose (Anser Huang AC, Lin WC, Horng YM, Rouvier R, Huang CW. 2003. fabalis) and White-fronted goose (Anser albifrons) in Junam Female-specific DNA sequences in geese. Br Poult Sci. reservoirs. Korea. Bull Korea Inst Ornithol. 4:1–24. (in Korean). 44:359–364. Quinn TW, Shields GF, Wilson AC. 1991. Affinities of the Karmiris I, Papachristou T, Platis P, Kazantzidis S. 2014. The diet Hawaiian goose based on two types of mitochondrial DNA of the wintering Lesser White-fronted Goose in two wetlands data. Auk. 107:199–202. in Greece. Final Report of the action A5 of the LIFE10NAT/GR/ Rho PH, Yoon JH, Choi JK, Lee SW, Sou HJ. 2010. Habitat 000638 project ‘Safeguarding the Lesser White–fronted evaluation strategy for legally protected wild-birds in goose Fennoscandian population in key wintering and Korea. Seoul: ROK: Korea Environ Inst (in Korean). staging sites within the European flyway’. Thessaloniki, Robb GN, McDonald RA, Chamberlain DE, Reynolds SJ, Harrison Greece: Hellenic Agricultural Organisation ‘DEMETER’/Forest THE, Bearhop S. 2008. Winter feeding of birds increases pro- Research Institute. ductivity in the subsequent breeding season. Biol Lett. Kim BJ, Lee NS, Lee SD. 2011. Feeding diets of the Korean water 4:220–223. deer (Hydropotes inermis argyropus) based on a 202 bp rbcL Sacchi P, Soglia D, Maione S, Meneguz G, Campora M, Rasero R. sequence analysis. Conserv Genet. 12:851–856. 2004. A non-invasive test for sex identification in the short- Kim MK, Lee S, Lee H, Lee S. 2012. Molecular tools for species toed Eagle (Circaetus gallicus). Mol Cell Probes. 18:193–196. and sex identification in the mixed-species flocks of Bean Stafford JD, Kaminski RM, Reinecke KJ. 2010. Avian foods, fora- geese and white-fronted geese. Zool Sci. 29:761–765. ging and habitat conservation in world rice fields. Kim MK, Lee S, Lee SD. 2016. Habitat use and its implications for Waterbirds. 33:133–150. the conservation strategies for the overwintering popu- Stafford JD, Kaminski RM, Reinecke KJ, Manley SW. 2006. Waste lations of the Bean goose (Anser fabalis) and the white- rice for waterfowl in the Mississippi Alluvial Valley. J Wildl fronted goose (A. albifrons) in South Korea. Ornithol Sci. Manage. 70:61–69. 15:141–149. Stech M, Kolvoort E, Loonen MJJE, Vrieling K, Kruijer JD. 2011. Kleven O, Kroglund RT, Østnes JE. 2016. Isolation, characteriz- Bryophyte DNA sequences from faeces of an arctic herbi- ation and multiplex PCR development of Bean goose vore, barnacle goose (Branta leucopsis). Mol Ecol Res. (Anser fabalis) microsatellite loci. J Ornithol. 157:641–646. 11:404–408. Lim Y, Yoo KP, The Korean Society of Plant Parataxonomists, Syroechkovskiy Jr EE. 2006. Long-term declines in arctic goose Hyun JO. 2014. Floristic study of Daebudo Island. Korean J populations in Eastern Asia. In: GC Boere, CA Galbraith, DA Plant Res. 27:447–476. (in Korean). Stroud, editor. Waterbirds around the world. Edinburgh: Marrero P, Oliveira P, Nogales M. 2004. Diet of the endemic The Stationery Office; p. 649–662. Madeira Laurel Pigeon Columba trocaz in agricultural and Valentini A, Miquel C, Nawaz MA, Bellemain EVA, Coissac E, forest areas: implications for conservation. Bird Conserv Int. Pompanon F, Swenson JE, Gielly L, Cruaud C, Nascetti G, 14:165–172. et al. 2009. New perspectives in diet analysis based on Ministry of Environment. 2004.99∼04 comprehensive report on DNA barcoding and parallel pyrosequencing: the trnL winter migratory bird census (in Korean). Incheon: ROK: approach. Mol Ecol Res. 9:51–60. Ministry of Environment. Waits LP, Paetkau D. 2005. Noninvasive genetic sampling tools Ministry of Environment. 2009. Winter migratory bird census (in for wildlife biologists: a review of applications and rec- Korean). Incheon: ROK: Ministry of Environment. ommendations for accurate data collection. J Wildl Ministry of Environment. 2010. Winter migratory bird census (in Manage. 69:1419–1433. Korean). Incheon: ROK: Ministry of Environment. Yoo SH, Kim IK, Kang TH, Yu JP, Lee SW, Lee HS. 2008. Wintering Ministry of Environment. 2011. Winter migratory bird census (in bird community in Cheonsu bay and the relationship with Korean). Incheon: ROK: Ministry of Environment. food resources. Korean J Env Eco. 22:301–308 (in Korean).
http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png
Animal Cells and Systems
Taylor & Francis
http://www.deepdyve.com/lp/taylor-francis/a-preliminary-analysis-of-the-diet-composition-of-overwintering-bean-sMcxs4DgUM
