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Ingvaldsen EW, Østnes JE, Kleven O, Davey M, Fossøy F, Nilsen EB. Fecal DNA metabarcoding reveals seasonal and annual variation in willow ptarmigan diet. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231518. [PMID: 38420626 PMCID: PMC10898975 DOI: 10.1098/rsos.231518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024]
Abstract
Understanding spatio-temporal variation in the diet of alpine herbivores is important to predict how a changing climate will affect these species in the future. We examined the spatio-temporal variation in willow ptarmigan (Lagopus l. lagopus) diet using DNA metabarcoding of fecal pellets sampled from winter to early summer over three consecutive years. Furthermore, we assessed how snow cover and vegetation phenology affected diet variation. We also investigated sex differences in diet composition. We identified 18 important diet taxa and the genera Betula, Vaccinium and Empetrum occurred most frequently. Diet composition and richness varied within and between years. Seasonally, there was a shift from a narrow winter diet dominated by trees and dwarf shrubs to a broader spring diet with more nutritious field vegetation. This seasonal progression differed among years. The temporal variation in diet was better explained by day of year than by snow cover and vegetation phenology. Females had a more diverse diet than males, but there were no sex differences in diet composition. Our results demonstrate that metabarcoding of fecal samples provides the opportunity to assess factors affecting diet composition of species in alpine ecosystems in the context of a changing climate.
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Affiliation(s)
- Elise W. Ingvaldsen
- Faculty of Biosciences and Aquaculture, Nord University, 7713 Steinkjer, Norway
| | - Jan E. Østnes
- Faculty of Biosciences and Aquaculture, Nord University, 7713 Steinkjer, Norway
| | - Oddmund Kleven
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | - Marie Davey
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | - Frode Fossøy
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | - Erlend B. Nilsen
- Faculty of Biosciences and Aquaculture, Nord University, 7713 Steinkjer, Norway
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
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Volmer JG, Soo RM, Evans PN, Hoedt EC, Astorga Alsina AL, Woodcroft BJ, Tyson GW, Hugenholtz P, Morrison M. Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated. BMC Biol 2023; 21:59. [PMID: 36949471 PMCID: PMC10035134 DOI: 10.1186/s12915-023-01524-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/20/2023] [Indexed: 03/24/2023] Open
Abstract
BACKGROUND With an increasing interest in the manipulation of methane produced from livestock cultivation, the microbiome of Australian marsupials provides a unique ecological and evolutionary comparison with 'low-methane' emitters. Previously, marsupial species were shown to be enriched for novel lineages of Methanocorpusculum, as well as Methanobrevibacter, Methanosphaera, and Methanomassiliicoccales. Despite sporadic reports of Methanocorpusculum from stool samples of various animal species, there remains little information on the impacts of these methanogens on their hosts. RESULTS Here, we characterise novel host-associated species of Methanocorpusculum, to explore unique host-specific genetic factors and their associated metabolic potential. We performed comparative analyses on 176 Methanocorpusculum genomes comprising 130 metagenome-assembled genomes (MAGs) recovered from 20 public animal metagenome datasets and 35 other publicly available Methanocorpusculum MAGs and isolate genomes of host-associated and environmental origin. Nine MAGs were also produced from faecal metagenomes of the common wombat (Vombatus ursinus) and mahogany glider (Petaurus gracilis), along with the cultivation of one axenic isolate from each respective animal; M. vombati (sp. nov.) and M. petauri (sp. nov.). CONCLUSIONS Through our analyses, we substantially expand the available genetic information for this genus by describing the phenotypic and genetic characteristics of 23 host-associated species of Methanocorpusculum. These lineages display differential enrichment of genes associated with methanogenesis, amino acid biosynthesis, transport system proteins, phosphonate metabolism, and carbohydrate-active enzymes. These results provide insights into the differential genetic and functional adaptations of these novel host-associated species of Methanocorpusculum and suggest that this genus is ancestrally host-associated.
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Affiliation(s)
- James G Volmer
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, 4102, Australia
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, 4102, Australia
| | - Rochelle M Soo
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, University of Queensland, Saint Lucia, 4072, Australia
| | - Paul N Evans
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, University of Queensland, Saint Lucia, 4072, Australia
| | - Emily C Hoedt
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, 4102, Australia
- Current Address: NHMRC Centre of Research Excellence (CRE) in Digestive Health, Hunter Medical Research Institute (HMRI), Newcastle, NSW, Australia
| | - Ana L Astorga Alsina
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, 4102, Australia
| | - Benjamin J Woodcroft
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, 4102, Australia
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, 4102, Australia
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, University of Queensland, Saint Lucia, 4072, Australia
| | - Mark Morrison
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, 4102, Australia.
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Watts SH, Jump AS. The benefits of mountain woodland restoration. Restor Ecol 2022. [DOI: 10.1111/rec.13701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sarah H. Watts
- University of Stirling. Biological and Environmental Sciences, Faculty of Natural Sciences University of Stirling UK
| | - Alistair S. Jump
- University of Stirling. Biological and Environmental Sciences, Faculty of Natural Sciences University of Stirling UK
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Fujii T, Ueno K, Shirako T, Nakamura M, Minami M. Identification of Lagopus muta japonica food plant resources in the Northern Japan Alps using DNA metabarcoding. PLoS One 2022; 17:e0252632. [PMID: 35271584 PMCID: PMC8912148 DOI: 10.1371/journal.pone.0252632] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 01/11/2022] [Indexed: 01/04/2023] Open
Abstract
DNA metabarcoding was employed to identify plant-derived food resources for the Japanese rock ptarmigan (Lagopus muta japonica), which is registered as a natural living monument in Japan, in the Northern Japanese Alps in Toyama Prefecture, Japan, in July to October, 2015-2018. DNA metabarcoding using high-throughput sequencing (HTS) of rbcL and ITS2 sequences from alpine plants found in ptarmigan fecal samples collected in the study area. The obtained sequences were analyzed using a combination of a constructed local database and the National Center for Biotechnology Information (NCBI) database, revealed that a total of 53 plant taxa were food plant resources for ptarmigans. Of these plant taxa, 49 could be assigned to species (92.5%), three to genus (5.7%), and one to family (1.9%). Of the 23 plant families identified from the 105 fecal samples collected, the dominant families throughout all collection periods were Ericaceae (99.0% of 105 fecal samples), followed by Rosaceae (42.9%), Apiaceae (35.2%), and Poaceae (21.0%). In all of the fecal samples examined, the most frequently encountered plant species were Vaccinium ovalifolium var. ovalifolium (69.5%), followed by Empetrum nigrum var. japonicum (68.6%), Kalmia procumbens (42.9%), Tilingia ajanensis (34.3%) and V. uliginosum var. japonicum (34.3%). A rarefaction analysis for each collection period in the study revealed that the food plant resources found in the study area ranged from a minimum of 87.0% in July to a maximum of 97.5% in September, and that 96.4% of the food plant taxa were found throughout the study period. The findings showed that DNA metabarcoding using HTS to construct a local database of rbcL and ITS2 sequences in conjunction with rbcL and ITS2 sequences deposited at the NCBI, as well as rarefaction analysis, are well suited to identifying the dominant food plants in the diet of Japanese rock ptarmigans. In the windswept alpine dwarf shrub community found in the study area, dominant taxa in the Ericaceae family were the major food plant s for Japanese rock ptarmigans from July to October. This plant community therefore needs to be conserved in order to protect the food resources of Japanese rock ptarmigans in the region.
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Affiliation(s)
- Taichi Fujii
- Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Kaoru Ueno
- Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Tomoyasu Shirako
- Institute of Environmental Ecology, IDEA Consultants, Inc., Riemon, Yaizu, Shizuoka, Japan
| | - Masatoshi Nakamura
- Institute of Environmental Ecology, IDEA Consultants, Inc., Riemon, Yaizu, Shizuoka, Japan
| | - Motoyasu Minami
- Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
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Ismaili B, Diouri M, Ouijja A. Getting the dietary knowledge to restore a missing species: seasonal diet of Atlas deer Cervus elaphus barbarus in Tazekka National Park, Morocco. WILDLIFE BIOLOGY 2018. [DOI: 10.2981/wlb.00387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Brahim Ismaili
- B. Ismaili , No. 140, Ex-Pépinière des eaux et forêts, BP 35000, Taza, Morroco
| | - Mohammed Diouri
- M. Doiuri (http://orcid.org/00000003-1242-5746), BVRV Research Team, Biology Dept, Moulay Ismail Uni
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García-González R, Aldezabal A, Laskurain NA, Margalida A, Novoa C. Influence of Snowmelt Timing on the Diet Quality of Pyrenean Rock Ptarmigan (Lagopus muta pyrenaica): Implications for Reproductive Success. PLoS One 2016; 11:e0148632. [PMID: 26849356 PMCID: PMC4746074 DOI: 10.1371/journal.pone.0148632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 01/21/2016] [Indexed: 11/18/2022] Open
Abstract
The Pyrenean rock ptarmigan (Lagopus muta pyrenaica) is the southernmost subspecies of the species in Europe and is considered threatened as a consequence of changes in landscape, human pressure, climate change, and low genetic diversity. Previous studies have shown a relationship between the date of snowmelt and reproductive success in the Pyrenean ptarmigan. It is well established that birds laying early in the breeding season have higher reproductive success, but the specific mechanism for this relationship is debated. We present an explicative model of the relationship between snowmelt date and breeding success mediated by food quality for grouse in alpine environments. From microhistological analyses of 121 faecal samples collected during three years in the Canigou Massif (Eastern Pyrenees), and the assessment of the chemical composition of the main dietary components, we estimated the potential quality of individual diets. Potential dietary quality was correlated with free-urate faecal N, a proxy of the digestible protein content ingested by ptarmigan, and both were correlated with phenological stage of consumed plants, which in turn depends on snowmelt date. Our findings suggest that the average snowmelt date is subject to a strong interannual variability influencing laying date. In years of early snowmelt, hens benefit from a longer period of high quality food resources potentially leading to a higher breeding success. On the contrary, in years of late snowmelt, hens begin their breeding period in poorer nutrient condition because the peaks of protein content of their main food items are delayed with respect to laying date, hence reducing breeding performance. We discuss the possible mismatch between breeding and snowmelt timing.
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Affiliation(s)
| | - Arantza Aldezabal
- Plant Biology and Ecology Department, Basque Country University, Bilbao, Spain
| | | | - Antoni Margalida
- Department of Animal Production, Division of Wildlife, Faculty of Life Sciences and Engineering, University of Lleida, Lleida, Spain
- Division of Conservation Biology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- * E-mail:
| | - Claude Novoa
- Office National de la Chasse et de la Faune Sauvage, Prades, France
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