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Mondino A, Crovadore J, Lefort F, Ursenbacher S. Impact of invading species on biodiversity: Diet study of the green whip snake’s (Hierophis viridiflavus, L. 1789) in Switzerland. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Mohd Salleh MH, Esa Y, Ngalimat MS, Chen PN. Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis. PeerJ 2022; 10:e12970. [PMID: 35368336 PMCID: PMC8973471 DOI: 10.7717/peerj.12970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/30/2022] [Indexed: 01/11/2023] Open
Abstract
Southern River Terrapin, Batagur affinis, is a freshwater turtle listed as critically endangered on the IUCN Red List since 2000. Many studies suggest that faecal DNA metabarcoding can shield light on the host-associated microbial communities that play important roles in host health. Thus, this study aimed to characterise and compare the faecal bacterial community between captive and wild B. affinis using metabarcoding approaches. A total of seven faeces samples were collected from captive (N = 5) and wild (N = 2) adult B. affinis aseptically, crossing the East and West coast of peninsular Malaysia. The DNA was extracted from the faeces samples, and the 16S rRNA gene (V3-V4 region) was amplified using polymerase chain reaction (PCR). The amplicon was further analysed using SILVA and DADA2 pipelines. In total, 297 bacterial communities taxonomic profile (phylum to genus) were determined. Three phyla were found in high abundance in all faeces samples, namely Firmicutes (38.69%), Bacteroidetes (24.52%), and Fusobacteria (6.95%). Proteobacteria were detected in all faeces samples (39.63%), except the wild sample, KBW3. Under genus level, Cetobacteriumwas found as the most abundant genus (67.79%), followed by Bacteroides (24.56%) and Parabacteroides (21.78%). The uncultured genus had the highest abundance (88.51%) even though not detected in the BK31 and KBW2 samples. The potential probiotic genera (75.00%) were discovered to be more dominant in B. affinis faeces samples. Results demonstrated that the captive B. affinis faeces samples have a greater bacterial variety and richness than wild B. affinis faeces samples. This study has established a starting point for future investigation of the gut microbiota of B. affinis.
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Affiliation(s)
- Mohd Hairul Mohd Salleh
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia,Royal Malaysian Customs Department, Presint 2, Putrajaya, Malaysia
| | - Yuzine Esa
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia,International Institute of Aquaculture and Aquatic Sciences, Universiti Putra Malaysia, Port Dickson, Negeri Sembilan, Malaysia
| | - Mohamad Syazwan Ngalimat
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Pelf Nyok Chen
- Turtle Conservation Society of Malaysia, Kemaman, Terengganu, Malaysia
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Tercel MPTG, Moorhouse‐Gann RJ, Cuff JP, Drake LE, Cole NC, Goder M, Mootoocurpen R, Symondson WOC. DNA metabarcoding reveals introduced species predominate in the diet of a threatened endemic omnivore, Telfair's skink ( Leiolopisma telfairii). Ecol Evol 2022; 12:e8484. [PMID: 35127020 PMCID: PMC8794715 DOI: 10.1002/ece3.8484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 12/04/2022] Open
Abstract
Introduced species can exert disproportionately negative effects on island ecosystems, but their potential role as food for native consumers is poorly studied. Telfair's skinks are endemic omnivores living on Round Island, Mauritius, a globally significant site of biodiversity conservation. We aimed to determine the dietary diversity and key trophic interactions of Telfair's skinks, whether introduced species are frequently consumed, and if diet composition changes seasonally between male and female skinks. We used DNA metabarcoding of skink fecal samples to identify animals (COI) and plants (ITS2) consumed by skinks. There were 389 dietary presence counts belonging to 77 dietary taxa found across the 73 Telfair's skink fecal samples. Introduced taxa were cumulatively consumed more frequently than other categories, accounting for 49.4% of all detections, compared to cryptogenic (20.6%), native (20.6%), and endemic taxa (9.5%). The most frequently consumed introduced species was the ant, Pheidole megacephala, present in 40% of samples. Blue latan palm, Latania loddigesii, was the most frequently consumed endemic species, present in 33% of samples but was only detected in the dry season, when fruits are produced. We found a strong seasonal difference in diet composition explained by the presence of certain plant species solely or primarily in one season and a marked increase in the consumption of animal prey in the dry season. Male and female skinks consumed several taxa at different frequencies. These results present a valuable perspective on the role of introduced species in the trophic network of their invaded ecosystem. Both native and introduced species provide nutritional resources for skinks, and this may have management implications in the context of species conservation and island restoration.
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Affiliation(s)
| | - Rosemary J. Moorhouse‐Gann
- School of BiosciencesCardiff UniversityCardiffUK
- Durrell Wildlife Conservation TrustTrinityJersey
- Department of Animal & Plant SciencesNERC Biomolecular Analysis FacilitySheffieldUK
| | - Jordan P. Cuff
- School of BiosciencesCardiff UniversityCardiffUK
- Rothamsted Insect Survey, Rothamsted ResearchHarpendenUK
| | | | - Nik C. Cole
- Durrell Wildlife Conservation TrustTrinityJersey
- Mauritian Wildlife FoundationVacoasMauritius
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Ducotterd C, Crovadore J, Lefort F, Rubin JF, Ursenbacher S. A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle (Emys orbicularis, L. 1758). Mol Ecol Resour 2020; 21:433-447. [PMID: 33047508 PMCID: PMC7821331 DOI: 10.1111/1755-0998.13277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 08/31/2020] [Accepted: 10/01/2020] [Indexed: 01/16/2023]
Abstract
High‐throughput sequencing has become an accurate method for the identification of species present in soil, water, faeces, gut or stomach contents. However, information at the species level is limited due to the choice of short barcodes and based on the idea that DNA is too degraded to allow longer sequences to be amplified. We have therefore developed a long DNA metabarcoding method based on the sequencing of short reads followed by de novo assembly, which can precisely identify the taxonomic groups of organisms associated with complex diets, such as omnivorous individuals. The procedure includes 11 different primer pairs targeting the COI gene, the large subunit of the ribulose‐1,5‐bisphosphate carboxylase gene, the maturase K gene, the 28S rRNA and the trnL‐trnF chloroplastic region. We validated this approach using 32 faeces samples from an omnivorous reptile, the European pond turtle (Emys orbicularis, L. 1758). This metabarcoding approach was assessed using controlled experiments including mock communities and faecal samples from captive feeding trials. The method allowed us to accurately identify prey DNA present in the diet of the European pond turtles to the species level in most of the cases (82.4%), based on the amplicon lengths of multiple markers (168–1,379 bp, average 546 bp), and produced by de novo assembly. The proposed approach can be adapted to analyse various diets, in numerous conservation and ecological applications. It is consequently appropriate for detecting fine dietary variations among individuals, populations and species as well as for the identification of rare food items.
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Affiliation(s)
- Charlotte Ducotterd
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Centre Emys, Association de Protection et Récupération des Tortues, Chavornay, Switzerland.,La Maison de la Rivière, Tolochenaz, Switzerland.,HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Jussy, Switzerland
| | - Julien Crovadore
- HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Jussy, Switzerland
| | - François Lefort
- HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Jussy, Switzerland
| | - Jean-François Rubin
- La Maison de la Rivière, Tolochenaz, Switzerland.,HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Jussy, Switzerland
| | - Sylvain Ursenbacher
- Department of Environmental Sciences, Section of Conservation Biology, University of Basel, Basel, Switzerland.,info fauna - Centre Suisse de Cartographie de la Faune (CSCF) and Centre de coordination pour les reptiles et les amphibiens de Suisse (Karch), Neuchâtel, Switzerland
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