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Joakim RL, Irham M, Haryoko T, Rowe KMC, Dalimunthe Y, Anita S, Achmadi AS, McGuire JA, Perkins S, Bowie RCK. Geography and elevation as drivers of cloacal microbiome assemblages of a passerine bird distributed across Sulawesi, Indonesia. Anim Microbiome 2023; 5:4. [PMID: 36647179 PMCID: PMC9841722 DOI: 10.1186/s42523-022-00219-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 12/13/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Empirical field studies allow us to view how ecological and environmental processes shape the biodiversity of our planet, but collecting samples in situ creates inherent challenges. The majority of empirical vertebrate gut microbiome research compares multiple host species against abiotic and biotic factors, increasing the potential for confounding environmental variables. To minimize these confounding factors, we focus on a single species of passerine bird found throughout the geologically complex island of Sulawesi, Indonesia. We assessed the effects of two environmental factors, geographic Areas of Endemism (AOEs) and elevation, as well as host sex on the gut microbiota assemblages of the Sulawesi Babbler, Pellorneum celebense, from three different mountains across the island. Using cloacal swabs, high-throughput-amplicon sequencing, and multiple statistical models, we identified the core microbiome and determined the signal of these three factors on microbial composition. RESULTS The five most prevalent bacterial phyla within the gut microbiome of P. celebense were Proteobacteria (32.6%), Actinobacteria (25.2%), Firmicutes (22.1%), Bacteroidetes (8.7%), and Plantomycetes (2.6%). These results are similar to those identified in prior studies of passeriform microbiomes. Overall, microbiota diversity decreased as elevation increased, irrespective of sex or AOE. A single ASV of Clostridium was enriched in higher elevation samples, while lower elevation samples were enriched with the genera Perlucidibaca (Family Moraxellaceae), Lachnoclostridium (Family Lachnospiraceae), and an unidentified species in the Family Pseudonocardiaceae. CONCLUSIONS While the core microbiota families recovered here are consistent with other passerine studies, the decreases in diversity as elevation increases has only been seen in non-avian hosts. Additionally, the increased abundance of Clostridium at high elevations suggests a potential microbial response to lower oxygen levels. This study emphasizes the importance of incorporating multiple statistical models and abiotic factors such as elevation in empirical microbiome research, and is the first to describe an avian gut microbiome from the island of Sulawesi.
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Affiliation(s)
- Rachael L. Joakim
- grid.254250.40000 0001 2264 7145Department of Biology, The City College of New York, 160 Convent Avenue, New York, NY 10031 USA ,grid.253482.a0000 0001 0170 7903The Graduate Center of The City University of New York, Biology Program, 365 5Th Ave, New York, NY 10016 USA ,grid.241963.b0000 0001 2152 1081Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024 USA ,grid.241963.b0000 0001 2152 1081The Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024 USA
| | - Mohammad Irham
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Karen M. C. Rowe
- grid.436717.00000 0004 0500 6540Sciences Department, Museums Victoria, Carlton, VIC Australia ,grid.1008.90000 0001 2179 088XBioSciences Department, University of Melbourne, Parkville, VIC Australia
| | - Yohanna Dalimunthe
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Syahfitri Anita
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Anang S. Achmadi
- Museum Zoologicum Bogoriense, Research Centre for Biology, National Research and Innovation Agency, Jl. Raya Jakarta - Bogor Km 46, Cibinong, 16911 Indonesia
| | - Jimmy A. McGuire
- grid.47840.3f0000 0001 2181 7878Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720 USA
| | - Susan Perkins
- grid.254250.40000 0001 2264 7145Department of Biology, The City College of New York, 160 Convent Avenue, New York, NY 10031 USA ,grid.253482.a0000 0001 0170 7903The Graduate Center of The City University of New York, Biology Program, 365 5Th Ave, New York, NY 10016 USA
| | - Rauri C. K. Bowie
- grid.47840.3f0000 0001 2181 7878Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720 USA
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Sosa V, Ornelas JF, Ramírez-Barahona S, Gándara E. Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica. PeerJ 2016; 4:e2696. [PMID: 27896030 PMCID: PMC5119233 DOI: 10.7717/peerj.2696] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 10/18/2016] [Indexed: 12/27/2022] Open
Abstract
Background Cloud forests, characterized by a persistent, frequent or seasonal low-level cloud cover and fragmented distribution, are one of the most threatened habitats, especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests, and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted species remained in situ or expanded to the lowlands during glacial cycles and contracted allopatrically during the interglacials. Although the observed genetic signals of population size changes of cloud forest-adapted species including tree ferns correspond to predicted changes by Pleistocene climate change dynamics, the observed patterns of intraspecific lineage divergence showed temporal incongruence. Methods Here we combined phylogenetic analyses, ancestral area reconstruction, and divergence time estimates with climatic and altitudinal data (environmental space) for phenotypic traits of tree fern species to make inferences about evolutionary processes in deep time. We used phylogenetic Bayesian inference and geographic and altitudinal distribution of tree ferns to investigate ancestral area and elevation and environmental preferences of Mesoamerican tree ferns. The phylogeny was then used to estimate divergence times and ask whether the ancestral area and elevation and environmental shifts were linked to climatic events and historical climatic preferences. Results Bayesian trees retrieved Cyathea, Alsophyla, Gymnosphaera and Sphaeropteris in monophyletic clades. Splits for species in these genera found in Mesoamerican cloud forests are recent, from the Neogene to the Quaternary, Australia was identified as the ancestral area for the clades of these genera, except for Gymnosphaera that was Mesoamerica. Climate tolerance was not divergent from hypothesized ancestors for the most significant variables or elevation. For elevational shifts, we found repeated change from low to high elevations. Conclusions Our data suggest that representatives of Cyatheaceae main lineages migrated from Australia to Mesoamerican cloud forests in different times and have persisted in these environmentally unstable areas but extant species diverged recentrly from their ancestors.
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Affiliation(s)
- Victoria Sosa
- Departamento de Biología Evolutiva, Instituto de Ecología AC, Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico
| | - Juan Francisco Ornelas
- Departamento de Biología Evolutiva, Instituto de Ecología AC, Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico
| | - Santiago Ramírez-Barahona
- Departamento de Biología Evolutiva, Instituto de Ecología AC, Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico
| | - Etelvina Gándara
- Departamento de Biología Evolutiva, Instituto de Ecología AC, Carretera antigua a Coatepec, El Haya, Xalapa, Veracruz, Mexico.,Instituto de Ciencias/Herbario y Jardín Botánico, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
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