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Liukkonen M, Muriel J, Martínez-Padilla J, Nord A, Pakanen VM, Rosivall B, Tilgar V, van Oers K, Grond K, Ruuskanen S. Seasonal and environmental factors contribute to the variation in the gut microbiome: A large-scale study of a small bird. J Anim Ecol 2024. [PMID: 39041321 DOI: 10.1111/1365-2656.14153] [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: 11/14/2023] [Accepted: 06/25/2024] [Indexed: 07/24/2024]
Abstract
Environmental variation can shape the gut microbiome, but broad/large-scale data on among and within-population heterogeneity in the gut microbiome and the associated environmental factors of wild populations is lacking. Furthermore, previous studies have limited taxonomical coverage, and knowledge about wild avian gut microbiomes is still scarce. We investigated large-scale environmental variation in the gut microbiome of wild adult great tits across the species' European distribution range. We collected fecal samples to represent the gut microbiome and used the 16S rRNA gene sequencing to characterize the bacterial gut microbiome. Our results show that gut microbiome diversity is higher during winter and that there are compositional differences between winter and summer gut microbiomes. During winter, individuals inhabiting mixed forest habitat show higher gut microbiome diversity, whereas there was no similar association during summer. Also, temperature was found to be a small contributor to compositional differences in the gut microbiome. We did not find significant differences in the gut microbiome among populations, nor any association between latitude, rainfall and the gut microbiome. The results suggest that there is a seasonal change in wild avian gut microbiomes, but that there are still many unknown factors that shape the gut microbiome of wild bird populations.
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Affiliation(s)
- Martta Liukkonen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Jaime Muriel
- Department of Biology, University of Turku, Turku, Finland
| | - Jesús Martínez-Padilla
- Department of Biodiversity Conservation and Ecosystem Restoration, Pyrenean Institute of Ecology (IPE-CSIC), Jaca, Spain
| | - Andreas Nord
- Department of Biology, Lund University, Lund, Sweden
| | | | - Balázs Rosivall
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Vallo Tilgar
- Department of Zoology, Tartu University, Tartu, Estonia
| | - Kees van Oers
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Kirsten Grond
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, Alaska, USA
| | - Suvi Ruuskanen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Department of Biology, University of Turku, Turku, Finland
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2
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Mistrick J, Kipp EJ, Weinberg SI, Adams CC, Larsen PA, Craft ME. Microbiome diversity and zoonotic bacterial pathogen prevalence in Peromyscus mice from agricultural landscapes and synanthropic habitat. Mol Ecol 2024; 33:e17309. [PMID: 38429967 DOI: 10.1111/mec.17309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/20/2024] [Accepted: 02/01/2024] [Indexed: 03/03/2024]
Abstract
Rodents are key reservoirs of zoonotic pathogens and play an important role in disease transmission to humans. Importantly, anthropogenic land-use change has been found to increase the abundance of rodents that thrive in human-built environments (synanthropic rodents), particularly rodent reservoirs of zoonotic disease. Anthropogenic environments also affect the microbiome of synanthropic wildlife, influencing wildlife health and potentially introducing novel pathogens. Our objective was to examine the effect of agricultural development and synanthropic habitat on microbiome diversity and the prevalence of zoonotic bacterial pathogens in wild Peromyscus mice to better understand the role of these rodents in pathogen maintenance and transmission. We conducted 16S amplicon sequencing on faecal samples using long-read nanopore sequencing technology to characterize the rodent microbiome. We compared microbiome diversity and composition between forest and synanthropic habitats in agricultural and undeveloped landscapes and screened for putative pathogenic bacteria. Microbiome richness, diversity, and evenness were higher in the agricultural landscape and synanthropic habitat compared to undeveloped-forest habitat. Microbiome composition also differed significantly between agricultural and undeveloped landscapes and forest and synanthropic habitats. We detected overall low diversity and abundance of putative pathogenic bacteria, though putative pathogens were more likely to be found in mice from the agricultural landscape. Our findings show that landscape- and habitat-level anthropogenic factors affect Peromyscus microbiomes and suggest that landscape-level agricultural development may be important to predict zoonotic pathogen prevalence. Ultimately, understanding how anthropogenic land-use change and synanthropy affect rodent microbiomes and pathogen prevalence is important to managing transmission of rodent-borne zoonotic diseases to humans.
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Affiliation(s)
- Janine Mistrick
- Department of Ecology, Evolution and Behavior, College of Biological Sciences, University of Minnesota, St. Paul, Minnesota, USA
| | - Evan J Kipp
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Sarah I Weinberg
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Collin C Adams
- Itasca Biological Station and Laboratories, University of Minnesota, Lake Itasca, Minnesota, USA
| | - Peter A Larsen
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Meggan E Craft
- Department of Ecology, Evolution and Behavior, College of Biological Sciences, University of Minnesota, St. Paul, Minnesota, USA
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Wang Z, Zhang E, Tang Y, Wu J, Muhammad S, Shang P, Zong C, Rong K, Ma J. Comparative analysis of the intestinal microbiota of black-necked cranes ( Grus nigricollis) in different wintering areas. Front Cell Infect Microbiol 2024; 13:1302785. [PMID: 38317791 PMCID: PMC10840423 DOI: 10.3389/fcimb.2023.1302785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/13/2023] [Indexed: 02/07/2024] Open
Abstract
Fecal microbiota is essential for host health because it increases digestive effectiveness. The crane species Grus nigricollis (G. nigricollis) is considered to be near threatened. The fecal microbial composition of crane is less understood, particularly in the Tibet, China. This study was performed to investigate the differences in fecal microbial composition and diversity of crane in different wintering areas using third-generation single-molecule real-time sequencing technology in the Tibet, China. According to the findings, 20 samples were used to generate 936 bacterial amplicon sequence variants (ASVs) and 1,800 fungal ASVs, only 4 bacterial ASVs and 20 fungal ASVs were shared in four distinct locations. Firmicutes were the dominant bacterial phylum in all samples, and Ascomycota and Basidiomycota were the dominant fungal phylum. At the genus level, Lactobacillus was the dominant genus in Linzhi City (LZ), Shannan City (SN), and Lasa City (LS), whereas Megamonas was the dominant genus in Rikaze City (RKZ). Naganishia and Mycosphaerella were the dominant fungal genera in SN and RKZ. Mycosphaerella and Tausonia were the dominant fungal genera in LZ. Naganishia and Fusarium were the dominant fungal genera in LS. And the fecal microbial composition varied between the four groups, as shown by the underweighted pair-group method with arithmetic means and principal coordinates analysis. This study offers a theoretical basis for understanding the fecal microbial composition of crane.
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Affiliation(s)
- Zhongbin Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- Department of Resources and Environment, Tibet Agricultural and Animal Husbandry College, Linzhi, Tibet, China
| | - Erhao Zhang
- Department of Resources and Environment, Tibet Agricultural and Animal Husbandry College, Linzhi, Tibet, China
| | - Ying Tang
- Department of Resources and Environment, Tibet Agricultural and Animal Husbandry College, Linzhi, Tibet, China
| | - Jiujiu Wu
- Department of Resources and Environment, Tibet Agricultural and Animal Husbandry College, Linzhi, Tibet, China
| | - Suliman Muhammad
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Peng Shang
- Department of Resources and Environment, Tibet Agricultural and Animal Husbandry College, Linzhi, Tibet, China
| | - Cheng Zong
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Ke Rong
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jianzhang Ma
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
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Jones TM, Llamas AP, Phillips JN. Phenotypic signatures of urbanization? Resident, but not migratory, songbird eye size varies with urban-associated light pollution levels. GLOBAL CHANGE BIOLOGY 2023; 29:6635-6646. [PMID: 37728032 DOI: 10.1111/gcb.16935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 09/21/2023]
Abstract
Urbanization now exposes large portions of the earth to sources of anthropogenic disturbance, driving rapid environmental change and producing novel environments. Changes in selective pressures as a result of urbanization are often associated with phenotypic divergence; however, the generality of phenotypic change remains unclear. In this study, we examined whether morphological phenotypes in two residential species (Carolina Wren [Thryothorus ludovicianus] and Northern Cardinal [Cardinalis cardinalis]) and two migratory species (Painted Bunting [Passerina ciris], and White-eyed Vireo [Vireo griseus]), differed between urban core and edge habitats in San Antonio, Texas, USA. More specifically, we examined whether urbanization, associated sensory pollution (light and noise) and brightness (open, bright areas cause by anthropogenic land use) influenced measures of avian body (mass and frame size) and lateral eye size. We found no differences in body size between urban core and edge habitats for all species except the Painted Bunting, in which core-urban individuals were smaller. Rather than a direct effect of urbanization, this was due to differences in age structure between habitats, with urban-core areas consisting of higher proportions of younger buntings which are, on average, smaller than older birds. Residential birds inhabiting urban-core areas had smaller eyes compared to their urban-edge counterparts, resulting from a negative association between eye size and light pollution and brightness across study sites; notably, we found no such association in the two migratory species. Our findings demonstrate how urbanization may indirectly influence phenotypes by altering population demographics and highlight the importance of accounting for age when assessing factors driving phenotypic change. We also provide some of the first evidence that birds may adapt to urban environments through changes in their eye morphology, demonstrating the need for future research into relationships among eye size, ambient light microenvironment use, and disassembly of avian communities as a result of urbanization.
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Affiliation(s)
- Todd M Jones
- Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, Texas, USA
- Migratory Bird Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Alfredo P Llamas
- Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, Texas, USA
| | - Jennifer N Phillips
- Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, Texas, USA
- School of the Environment, Washington State University, Pullman, Washington, USA
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5
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Stothart MR, Spina HA, Hotchkiss MZ, Ko W, Newman AEM. Seasonal dynamics in the mammalian microbiome between disparate environments. Ecol Evol 2023; 13:e10692. [PMID: 38111921 PMCID: PMC10726273 DOI: 10.1002/ece3.10692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 12/20/2023] Open
Abstract
Host-associated bacterial microbiomes can facilitate host acclimation to seasonal environmental change and are hypothesized to help hosts cope with recent anthropogenic environmental perturbations (e.g., landscape modification). However, it is unclear how recurrent and recent forms of environmental change interact to shape variation in the microbiome. The majority of wildlife microbiome research occurs within a single seasonal context. Meanwhile, the few studies of seasonal variation in the microbiome often restrict focus to a single environmental context. By sampling urban and exurban eastern grey squirrel populations in the spring, summer, autumn, and winter, we explored whether seasonal rhythms in the grey squirrel gut microbiome differed across environments using a 16S amplicon sequencing approach. Differences in the microbiome between urban and exurban squirrels persisted across most of the year, which we hypothesize is linked to anthropogenic food consumption, but we also observed similarities in the urban and exurban grey squirrel microbiome during the autumn, which we attribute to engrained seed caching instincts in preparation for the winter. Host behaviour and diet selection may therefore be capable of maintaining similarities in microbiome structure between disparate environments. However, the depletion of an obligate host mucin glycan specialist (Akkermansia) during the winter in both urban and exurban squirrels was among the strongest differential abundance patterns we observed. In summary, urban grey squirrels showed different seasonal patterns in their microbiome than squirrels from exurban forests; however, in some instances, host behaviour and physiological responses might be capable of maintaining similar microbiome responses across seasons.
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Affiliation(s)
- Mason R. Stothart
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
- Faculty of Veterinary MedicineUniversity of CalgaryCalgaryAlbertaCanada
| | - Hayley A. Spina
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
| | | | - Winnie Ko
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
| | - Amy E. M. Newman
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
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Chalifour BN, Elder LE, Li J. Diversity of gut microbiome in Rocky Mountainsnail across its native range. PLoS One 2023; 18:e0290292. [PMID: 38011083 PMCID: PMC10681204 DOI: 10.1371/journal.pone.0290292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 08/07/2023] [Indexed: 11/29/2023] Open
Abstract
The animal gut microbiome is often a key requirement for host nutrition, digestion, and immunity, and can shift in relation to host geography and environmental factors. However, ecological drivers of microbiome community assembly across large geographic ranges have rarely been examined in invertebrates. Oreohelix strigosa (Rocky Mountainsnail) is a widespread land snail found in heterogeneous environments across the mountainous western United States. It is ideally suited for biogeography studies due to its broad distribution, low migration, and low likelihood of passive transport via other animals. This study aims to uncover large-scale geographic shifts in the composition of O. strigosa gut microbiomes by using 16S rRNA gene sequencing on samples from across its native range. Additionally, we elucidate smaller-scale microbiome variation using samples collected only within Colorado. Results show that gut microbiomes vary significantly across broad geographic ranges. Several possible ecological drivers, including soil and vegetation composition, habitat complexity, habitat type, and human impact, collectively explained 27% of the variation across Coloradan O. strigosa gut microbiomes. Snail gut microbiomes show more similarity to vegetation than soil microbiomes. Gut microbial richness was highest in the rocky habitats and increased significantly in the most disturbed habitats (low complexity, high human impact), potentially indicating signs of dysbiosis in the snails' gut microbiomes. These small-scale environmental factors may be driving changes in O. strigosa gut microbiome composition seen across large-scale geography. This knowledge will also help us better understand how microbial associations influence species survival in diverse environments and aid wildlife conservation efforts.
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Affiliation(s)
- Bridget N. Chalifour
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Leanne E. Elder
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Jingchun Li
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
- Museum of Natural History, University of Colorado Boulder, Boulder, Colorado, United States of America
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7
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Solomon G, Love AC, Vaziri GJ, Harvey J, Verrett T, Chernicky K, Simons S, Albert L, Chaves JA, Knutie SA. Effect of urbanization and parasitism on the gut microbiota of Darwin's finch nestlings. Mol Ecol 2023; 32:6059-6069. [PMID: 37837269 DOI: 10.1111/mec.17164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/20/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023]
Abstract
Host-associated microbiota can be affected by factors related to environmental change, such as urbanization and invasive species. For example, urban areas often affect food availability for animals, which can change their gut microbiota. Invasive parasites can also influence microbiota through competition or indirectly through a change in the host immune response. These interacting factors can have complex effects on host fitness, but few studies have disentangled the relationship between urbanization and parasitism on an organism's gut microbiota. To address this gap in knowledge, we investigated the effects of urbanization and parasitism by the invasive avian vampire fly (Philornis downsi) on the gut microbiota of nestling small ground finches (Geospiza fuliginosa) on San Cristóbal Island, Galápagos. We conducted a factorial study in which we experimentally manipulated parasite presence in an urban and nonurban area. Faeces were then collected from nestlings to characterize the gut microbiota (i.e. bacterial diversity and community composition). Although we did not find an interactive effect of urbanization and parasitism on the microbiota, we did find main effects of each variable. We found that urban nestlings had lower bacterial diversity and different relative abundances of taxa compared to nonurban nestlings, which could be mediated by introduction of the microbiota of the food items or changes in host physiology. Additionally, parasitized nestlings had lower bacterial richness than nonparasitized nestlings, which could be mediated by a change in the immune system. Overall, this study advances our understanding of the complex effects of anthropogenic stressors on the gut microbiota of birds.
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Affiliation(s)
- Gabrielle Solomon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Connecticut, Storrs, USA
| | - Ashley C Love
- Department of Ecology and Evolutionary Biology, University of Connecticut, Connecticut, Storrs, USA
| | - Grace J Vaziri
- Department of Ecology and Evolutionary Biology, University of Connecticut, Connecticut, Storrs, USA
| | - Johanna Harvey
- Department of Ecology and Evolutionary Biology, University of Connecticut, Connecticut, Storrs, USA
| | - Taylor Verrett
- Department of Ecology and Evolutionary Biology, University of Connecticut, Connecticut, Storrs, USA
| | - Kiley Chernicky
- Department of Ecology and Evolutionary Biology, University of Connecticut, Connecticut, Storrs, USA
| | - Shelby Simons
- Department of Ecology and Evolutionary Biology, University of Connecticut, Connecticut, Storrs, USA
| | - Lauren Albert
- Department of Ecology and Evolutionary Biology, University of Connecticut, Connecticut, Storrs, USA
| | - Jaime A Chaves
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
- Galapagos Science Center, Puerto Baquerizo Moreno, Galapagos, Ecuador
- Department of Biology, San Francisco State University, California, San Francisco, USA
| | - Sarah A Knutie
- Department of Ecology and Evolutionary Biology, University of Connecticut, Connecticut, Storrs, USA
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
- Institute for Systems Genomics, University of Connecticut, Connecticut, Storrs, USA
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He Y, Zhang M, Dai C, Yu L. Comparison of the Gut Microbial Communities of Domestic and Wild Mallards ( Anas platyrhynchos) Based on High-Throughput Sequencing Technology. Animals (Basel) 2023; 13:2956. [PMID: 37760356 PMCID: PMC10525502 DOI: 10.3390/ani13182956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Mallards (Anas platyrhynchos) are currently one of the most popular species in rare bird breeding in several southern provinces of China, but there have been no studies comparing the gut microbial communities of domestic and wild mallards. In this study, 16S rRNA gene high-throughput sequencing technology was used to compare the composition and diversity of gut microbial communities in domestic and wild mallards. Alpha diversity analysis showed significant differences in gut microbial communities between the two groups of mallards, and the diversity and richness of gut microbial communities were significantly higher in wild mallards than in domestic mallards. Beta diversity analysis showed that the two groups of stool samples were mostly separated on the principal coordinate analysis (PCoA) plot. In domestic mallards, Firmicutes (68.0% ± 26.5%) was the most abundant bacterial phylum, followed by Proteobacteria (24.5% ± 22.9%), Bacteroidetes (3.1% ± 3.2%), Fusobacteria (2.2% ± 5.9%), and Actinobacteria (1.1% ± 1.8%). The dominant bacterial phyla in wild mallards were Firmicutes (79.0% ± 10.2%), Proteobacteria (12.9% ± 9.5%), Fusobacteria (3.4% ± 2.5%), and Bacteroidetes (2.8% ± 2.4%). At the genus level, a total of 10 dominant genera (Streptococcus, Enterococcus, Clostridium, Lactobacillus, Soilbacillus, Bacillus, Acinetobacter, Comamonas, Shigella, and Cetobacterium) with an average relative abundance greater than 1% were detected in the fecal samples of both groups. The average relative abundance of five potential pathogenic genera (Streptococcus, Enterococcus, Acinetobacter, Comamonas, and Shigella) was higher in domestic mallards than in wild mallards. The enrichment of pathogenic bacteria in the intestinal tract of domestic mallards should be of sufficient concern.
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Affiliation(s)
- Yaoyin He
- Animal Science and Technology College, Guangxi University, Nanning 530004, China; (Y.H.); (M.Z.)
| | - Minghui Zhang
- Animal Science and Technology College, Guangxi University, Nanning 530004, China; (Y.H.); (M.Z.)
| | - Chuanyin Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin 541006, China;
| | - Lijiang Yu
- Animal Science and Technology College, Guangxi University, Nanning 530004, China; (Y.H.); (M.Z.)
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García GO, Zumpano F, Mariano y Jelicich R, Favero M. Effect of urbanization on individual condition of a threatened seabird: the Olrog’s Gull Larus atlanticus. Urban Ecosyst 2023. [DOI: 10.1007/s11252-023-01347-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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10
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Neha SA, Salazar-Bravo J. Fine-scale spatial variation shape fecal microbiome diversity and composition in black-tailed prairie dogs (Cynomys ludovicianus). BMC Microbiol 2023; 23:51. [PMID: 36858951 PMCID: PMC9979494 DOI: 10.1186/s12866-023-02778-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/19/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Host associated gut microbiota are important in understanding the coevolution of host-microbe, and how they may help wildlife populations to adapt to rapid environmental changes. Mammalian gut microbiota composition and diversity may be affected by a variety of factors including geographic variation, seasonal variation in diet, habitat disturbance, environmental conditions, age, and sex. However, there have been few studies that examined how ecological and environmental factors influence gut microbiota composition in animals' natural environments. In this study, we explore how host habitat, geographical location and environmental factors affect the fecal microbiota of Cynomys ludovicianus at a small spatial scale. We collected fecal samples from five geographically distinct locations in the Texas Panhandle classified as urban and rural areas and analyzed them using high throughput 16S rRNA gene amplicon sequencing. RESULTS The results showed that microbiota of these fecal samples was largely dominated by the phylum Bacteroidetes. Fecal microbiome diversity and composition differed significantly across sampling sites and habitats. Prairie dogs inhabiting urban areas showed reduced fecal diversity due to more homogenous environment and, likely, anthropogenic disturbance. Urban prairie dog colonies displayed greater phylogenetic variation among replicates than those in rural habitats. Differentially abundant analysis revealed that bacterial species pathogenic to humans and animals were highly abundant in urban areas which indicates that host health and fitness might be negatively affected. Random forest models identified Alistipes shahii as the important species driving the changes in fecal microbiome composition. Despite the effects of habitat and geographic location of host, we found a strong correlation with environmental factors and that- average maximum temperature was the best predictor of prairie dog fecal microbial diversity. CONCLUSIONS Our findings suggest that reduction in alpha diversity in conjunction with greater dispersion in beta diversity could be indicative of declining host health in urban areas; this information may, in turn, help determine future conservation efforts. Moreover, several bacterial species pathogenic to humans and other animals were enriched in prairie dog colonies near urban areas, which may in turn adversely affect host phenotype and fitness.
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Affiliation(s)
- Sufia Akter Neha
- International Center for Arid and Semi-Arid Land Studies, Texas Tech University, Lubbock, TX, 79409, USA. .,Department of Biological Sciences, Texas Tech University, Lubbock, 79409, USA.
| | - Jorge Salazar-Bravo
- International Center for Arid and Semi-Arid Land Studies, Texas Tech University, Lubbock, TX, 79409, USA.,Department of Biological Sciences, Texas Tech University, Lubbock, 79409, USA
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11
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Holmes IA, Grundler MC. Phylogenetically under-dispersed gut microbiomes are not correlated with host genomic heterozygosity in a genetically diverse reptile community. Mol Ecol 2023; 32:258-274. [PMID: 36221927 PMCID: PMC9797449 DOI: 10.1111/mec.16733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 12/31/2022]
Abstract
While key elements of fitness in vertebrate animals are impacted by their microbiomes, the host genetic characteristics that factor into microbiome composition are not fully understood. Here, we correlate host genomic heterozygosity and gut microbiome phylogenetic diversity across a community of reptiles in southwestern New Mexico to test hypotheses about the behaviour of host genes that drive microbiome assembly. We find that microbiome communities are phylogenetically under-dispersed relative to random expectations, and that host heterozygosity is not correlated with microbiome diversity. Our analyses reinforce results from functional genomic work that identify conserved host immune and nonimmune genes as key players in microbiome assembly, rather than gene families that rely on heterozygosity for their function.
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Affiliation(s)
- Iris A. Holmes
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Cornell Institute of Host Microbe Interactions and Disease and Department of Microbiology, Cornell University, Ithaca, NY 14853 USA
| | - Michael C. Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095 USA
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12
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Vasconcelos DS, Harris DJ, Damas-Moreira I, Pereira A, Xavier R. Factors shaping the gut microbiome of five species of lizards from different habitats. PeerJ 2023; 11:e15146. [PMID: 37187519 PMCID: PMC10178224 DOI: 10.7717/peerj.15146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/09/2023] [Indexed: 05/17/2023] Open
Abstract
Background Host-gut microbiota interactions are complex and can have a profound impact on the ecology and evolution of both counterparts. Several host traits such as systematics, diet and social behavior, and external factors such as prey availability and local environment are known to influence the composition and diversity of the gut microbiota. Methods In this study, we investigate the influence of systematics, sex, host size, and locality/habitat on gut microbiota diversity in five lizard species from two different sites in Portugal: Podarcis bocagei and Podarcis lusitanicus, living in syntopy in a rural area in northern Portugal (Moledo); the invasive Podarcis siculus and the native Podarcis virescens, living in sympatry in an urbanized environment (Lisbon); and the invasive Teira dugesii also living in an urban area (Lisbon). We also infer the potential microbial transmission occurring between species living in sympatry and syntopy. To achieve these goals, we use a metabarcoding approach to characterize the bacterial communities from the cloaca of lizards, sequencing the V4 region of the 16S rRNA. Results Habitat/locality was an important factor explaining differences in gut bacterial composition and structure, with species from urbanized environments having higher bacterial diversity. Host systematics (i.e., species) influenced gut bacterial community structure only in lizards from the urbanized environment. We also detected a significant positive correlation between lizard size and gut bacterial alpha-diversity in the invasive species P. siculus, which could be due to its higher exploratory behavior. Moreover, estimates of bacterial transmission indicate that P. siculus may have acquired a high proportion of local microbiota after its introduction. These findings confirm that a diverse array of host and environmental factors can influence lizards' gut microbiota.
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Affiliation(s)
- Diana S. Vasconcelos
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão da Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO - Campus de Vairão, Vairão, Portugal
| | - D. James Harris
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão da Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO - Campus de Vairão, Vairão, Portugal
| | | | - Ana Pereira
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão da Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO - Campus de Vairão, Vairão, Portugal
| | - Raquel Xavier
- CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão da Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO - Campus de Vairão, Vairão, Portugal
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13
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Bridson C, Vellaniparambil L, Antwis RE, Müller W, Gilman RT, Rowntree JK. Genetic diversity of honeybee colonies predicts gut bacterial diversity of individual colony members. Environ Microbiol 2022; 24:5643-5653. [PMID: 35920034 PMCID: PMC10087737 DOI: 10.1111/1462-2920.16150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/18/2022] [Accepted: 07/22/2022] [Indexed: 01/13/2023]
Abstract
The gut microbiota of social bees is relatively simple and dominated by a set of core taxa found consistently in individuals around the world. Yet, variation remains and can affect host health. We characterized individual- and regional-scale variation in honeybee (Apis mellifera) gut microbiota from 64 colonies in North-West England by sequencing the V4 region of the 16S rRNA gene and asked whether microbiota were influenced by host genotype and landscape composition. We also characterized the genotypes of individual bees and the land cover surrounding each colony. The literature-defined core taxa dominated across the region despite the varied environments. However, there was variation in the relative abundance of core taxa, and colony membership explained much of this variation. Individuals from more genetically diverse colonies had more diverse microbiotas, but individual genetic diversity did not influence gut microbial diversity. There were weak trends for colonies in more similar landscapes to have more similar microbiota, and for bees from more urban landscapes to have less diverse microbiota. To our knowledge, this is the first report for any species that the gut bacterial communities of individuals are influenced by the genotypes of others in the population.
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Affiliation(s)
- Calum Bridson
- Faculty of Science and Engineering, University of Manchester, Manchester, UK.,Faculty of Biology Medicine and Health, Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK.,Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany.,Translational Lung Research Centre (TLRC), Heidelberg, Germany
| | - Latha Vellaniparambil
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
| | - Rachel E Antwis
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Werner Müller
- Faculty of Biology Medicine and Health, Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK.,Miltenyi Biotec, Bergisch Gladbach, Germany
| | - R Tucker Gilman
- Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Jennifer K Rowntree
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
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14
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Donald ML, Galbraith JA, Erastova DA, Podolyan A, Miller TEX, Dhami MK. Nectar resources affect bird-dispersed microbial metacommunities in suburban and rural gardens. Environ Microbiol 2022; 24:5654-5665. [PMID: 36102191 PMCID: PMC10087401 DOI: 10.1111/1462-2920.16159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/02/2022] [Indexed: 01/12/2023]
Abstract
As cities expand, understanding how urbanization affects biodiversity is a key ecological goal. Yet, little is known about how host-associated microbial diversity responds to urbanization. We asked whether communities of microbial (bacterial and fungal) in floral nectar and sugar-water feeders and vectored by nectar-feeding birds-thus forming a metacommunity-differed in composition and diversity between suburban and rural gardens. Compared to rural birds, we found that suburban birds vectored different and more diverse bacterial communities. These differences were not detected in the nectar of common plant species, suggesting that nectar filters microbial taxa and results in metacommunity convergence. However, when considering all the nectar sources present, suburban beta diversity was elevated compared to rural beta diversity due to turnover of bacterial taxa across a plant species and sugar-water feeders. While fungal metacommunity composition and beta diversity in nectar were similar between suburban and rural sites, alpha diversity was elevated in suburban sites, which mirrored the trend of increased fungal alpha diversity on birds. These results emphasize the interdependence of host, vector, and microbial diversity and demonstrate that human decisions can shape nectar microbial diversity in contrasting ways for bacteria and fungi.
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Affiliation(s)
- Marion L Donald
- Department of Biosciences, Rice University, Houston, Texas, USA.,Biocontrol & Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Josie A Galbraith
- Department of Natural Sciences, Auckland Museum, Auckland, New Zealand
| | - Daria A Erastova
- School of Biological Science, The University of Auckland, Auckland, New Zealand
| | - Anastasija Podolyan
- Biocontrol & Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Tom E X Miller
- Program in Ecology and Evolutionary Biology, Department of Biosciences, Rice University, Houston, Texas, USA
| | - Manpreet K Dhami
- Biocontrol & Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
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15
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Thie N, Corl A, Turjeman S, Efrat R, Kamath PL, Getz WM, Bowie RCK, Nathan R. Linking migration and microbiota at a major stopover site in a long-distance avian migrant. MOVEMENT ECOLOGY 2022; 10:46. [PMID: 36345043 PMCID: PMC9641824 DOI: 10.1186/s40462-022-00347-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Migration is one of the most physical and energetically demanding periods in an individual bird's life. The composition of the bird's gut or cloacal microbiota can temporarily change during migration, likely due to differences in diets, habitats and other environmental conditions experienced en route. However, how physiological condition, migratory patterns, and other drivers interact to affect microbiota composition of migratory birds is still unclear. We sampled the cloacal bacterial microbiota of a long-distance migrant, the steppe buzzard (Buteo buteo vulpinus), at an important spring stopover bottleneck in Eilat, Israel, after crossing the ca. 1800 km Sahara Desert. We examined whether diversity and composition of the cloacal microbiota varied with body condition, sex, movement patterns (i.e., arrival time and migration distance), and survival. Early arrival to Eilat was associated with better body condition, longer post-Eilat spring migration distance, higher microbial α-diversity, and differences in microbiota composition. Specifically, early arrivals had higher abundance of the phylum Synergistota and five genera, including Jonquetella and Peptococcus, whereas the phylum Proteobacteria and genus Escherichia-Shigella (as well as three other genera) were more abundant in later arrivals. While the differences in α-diversity and Escherichia-Shigella seem to be mainly driven by body condition, other compositional differences associated with arrival date could be indicators of longer migratory journeys (e.g., pre-fueling at wintering grounds or stopover habitats along the way) or migratory performance. No significant differences were found between the microbiota of surviving and non-surviving individuals. Overall, our results indicate that variation in steppe buzzard microbiota is linked to variation in migratory patterns (i.e., capture/arrival date) and body condition, highlighting the importance of sampling the microbiota of GPS-tracked individuals on multiple occasions along their migration routes to gain a more detailed understanding of the links between migration, microbiota, and health in birds.
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Affiliation(s)
- Nikki Thie
- Movement Ecology Lab, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Ammon Corl
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA
| | - Sondra Turjeman
- Movement Ecology Lab, The Hebrew University of Jerusalem, Jerusalem, Israel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ron Efrat
- Movement Ecology Lab, The Hebrew University of Jerusalem, Jerusalem, Israel
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Pauline L Kamath
- School of Food and Agriculture, University of Maine, Orono, ME, USA
| | - Wayne M Getz
- Department of Environmental Science Policy and Management, University of California, Berkeley, Berkeley, CA, USA
- School of Mathematical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ran Nathan
- Movement Ecology Lab, The Hebrew University of Jerusalem, Jerusalem, Israel.
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16
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Berlow M, Wada H, Derryberry EP. Experimental Exposure to Noise Alters Gut Microbiota in a Captive Songbird. MICROBIAL ECOLOGY 2022; 84:1264-1277. [PMID: 34783872 DOI: 10.1007/s00248-021-01924-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 11/09/2021] [Indexed: 05/20/2023]
Abstract
Noise pollution is an unprecedented evolutionary pressure on wild animals that can lead to alteration of stress hormone levels and changes in foraging behavior. Both corticosterone and feeding behavior can have direct effects on gut bacteria, as well as indirect effects through changes in gut physiology. Therefore, we hypothesized that exposure to noise will alter gut microbial communities via indirect effects on glucocorticoids and foraging behaviors. We exposed captive white-crowned sparrows to city-like noise and measured each individuals' corticosterone level, food intake, and gut microbial diversity at the end of four treatments (acclimation, noise, recovery, and control) using a balanced repeated measures design. We found evidence that noise acts to increase corticosterone and decrease food intake, adding to a growing body of research indicating noise exposure affects stress hormone levels and foraging behaviors. We also found evidence to support our prediction for a causal, positive relationship between noise exposure and gut microbial diversity, such that birds had higher measures of alpha diversity during noise exposure. These results help to explain previous findings that urban, free-living white-crowned sparrows have higher bacterial richness than rural sparrows. However, noise appeared to act directly on the gut microbiome or, more likely, through an unmeasured variable, rather than through indirect effects via corticosterone and food intake. Altogether, our study indicates that noise affects plasma corticosterone, feeding behavior, and the gut microbiome in a songbird and raises new questions as to the mechanism linking noise exposure to gut microbial diversity.
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Affiliation(s)
- Mae Berlow
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA.
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA.
| | - Haruka Wada
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA
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17
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Anders JL, Mychajliw AM, Moustafa MAM, Mohamed WMA, Hayakawa T, Nakao R, Koizumi I. Dietary niche breadth influences the effects of urbanization on the gut microbiota of sympatric rodents. Ecol Evol 2022; 12:e9216. [PMID: 36177145 PMCID: PMC9463044 DOI: 10.1002/ece3.9216] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 12/02/2022] Open
Abstract
Cities are among the most extreme forms of anthropogenic ecosystem modification, and urbanization processes exert profound effects on animal populations through multiple ecological pathways. Increased access to human‐associated food items may alter species' foraging behavior and diet, in turn modifying the normal microbial community of the gastrointestinal tract (GIT), ultimately impacting their health. It is crucial we understand the role of dietary niche breadth and the resulting shift in the gut microbiota as urban animals navigate novel dietary resources. We combined stable isotope analysis of hair and microbiome analysis of four gut regions across the GIT to investigate the effects of urbanization on the diet and gut microbiota of two sympatric species of rodents with different dietary niches: the omnivorous large Japanese field mouse (Apodemus speciosus) and the relatively more herbivorous gray red‐backed vole (Myodes rufocanus). Both species exhibited an expanded dietary niche width within the urban areas potentially attributable to novel anthropogenic foods and altered resource availability. We detected a dietary shift in which urban A. speciosus consumed more terrestrial animal protein and M. rufocanus more plant leaves and stems. Such changes in resource use may be associated with an altered gut microbial community structure. There was an increased abundance of the presumably probiotic Lactobacillus in the small intestine of urban A. speciosus and potentially pathogenic Helicobacter in the colon of M. rufocanus. Together, these results suggest that even taxonomically similar species may exhibit divergent responses to urbanization with consequences for the gut microbiota and broader ecological interactions.
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Affiliation(s)
- Jason L Anders
- Graduate School of Environmental Science Hokkaido University Sapporo Japan.,Department of Biosciences, Center for Ecological and Evolutionary Synthesis (CEES) University of Oslo Oslo Norway
| | - Alexis M Mychajliw
- Department of Biology Middlebury College Middlebury Vermont USA.,Department of Environmental Studies Middlebury College Middlebury Vermont USA
| | - Mohamed Abdallah Mohamed Moustafa
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Graduate School of Infectious Diseases Hokkaido University Sapporo Japan.,Department of Animal Medicine South Valley University Qena Egypt.,Department of Microbiology, Biochemistry and Molecular Genetics Rutgers New Jersey Medical School Newark New Jersey USA
| | - Wessam Mohamed Ahmed Mohamed
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Graduate School of Infectious Diseases Hokkaido University Sapporo Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science Hokkaido University Sapporo Japan.,Japan Monkey Center Inuyama Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Graduate School of Infectious Diseases Hokkaido University Sapporo Japan
| | - Itsuro Koizumi
- Faculty of Environmental Earth Science Hokkaido University Sapporo Japan
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18
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Sun F, Chen J, Liu K, Tang M, Yang Y. The avian gut microbiota: Diversity, influencing factors, and future directions. Front Microbiol 2022; 13:934272. [PMID: 35992664 PMCID: PMC9389168 DOI: 10.3389/fmicb.2022.934272] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
The gut microbiota is viewed as the “second genome” of animals, sharing intricate relationships with their respective hosts. Because the gut microbial community and its diversity are affected by many intrinsic and extrinsic factors, studying intestinal microbes has become an important research topic. However, publications are dominated by studies on domestic or captive birds, while research on the composition and response mechanism of environmental changes in the gut microbiota of wild birds remains scarce. Therefore, it is important to understand the co-evolution of host and intestinal bacteria under natural conditions to elucidate the diversity, maintenance mechanisms, and functions of gut microbes in wild birds. Here, the existing knowledge of gut microbiota in captive and wild birds is summarized, along with previous studies on the composition and function, research methods employed, and factors influencing the avian gut microbial communities. Furthermore, research hotspots and directions were also discussed to identify the dynamics of the avian gut microbiota, aiming to contribute to studies of avian microbiology in the future.
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19
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Lu Z, Li S, Wang M, Wang C, Meng D, Liu J. Comparative Analysis of the Gut Microbiota of Three Sympatric Terrestrial Wild Bird Species Overwintering in Farmland Habitats. Front Microbiol 2022; 13:905668. [PMID: 35928156 PMCID: PMC9343720 DOI: 10.3389/fmicb.2022.905668] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
The gut microbiota of wild birds are affected by complex factors, and cross-species transmission may pose challenges for the host to maintain stable gut symbionts. Farmland habitats are environments strongly manipulated by humans, and the environmental characteristics within a large area are highly consistent. These features provide the ideal natural conditions for conducting cross-species comparative studies on gut microbiota among wild birds. This study aimed to investigate and compare the gut microbiota of three common farmland-dependent bird species, Great Bustard (Otis tarda dybowskii), Common Crane (Grus grus), and Common Coot (Fulica atra), in a homogeneous habitat during the wintering period. The results indicated that under the combined action of similar influencing factors, the gut microbiota of different host species did not undergo adaptive convergence, maintained relatively independent structures, and exhibited host-driven signals. In addition, we also detected various pathogenic genera that may cause outbreaks of periodic infections among sympatric migratory birds. We conclude that phylosymbiosis may occur between some wild birds and their gut microbiota. Usage of non-invasive methods to monitor the changes in the gut microbiota of wild bird fecal samples has important implications for the conservation of endangered species.
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Affiliation(s)
- Zhiyuan Lu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- College of Life Sciences, Cangzhou Normal University, Cangzhou, China
| | - Sisi Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Min Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Can Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Derong Meng
- College of Life Sciences, Cangzhou Normal University, Cangzhou, China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- *Correspondence: Jingze Liu,
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20
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Maraci Ö, Corsini M, Antonatou-Papaioannou A, Jünemann S, Sudyka J, Di Lecce I, Caspers BA, Szulkin M. Changes to the gut microbiota of a wild juvenile passerine in a multidimensional urban mosaic. Sci Rep 2022; 12:6872. [PMID: 35477720 PMCID: PMC9046431 DOI: 10.1038/s41598-022-10734-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 04/06/2022] [Indexed: 02/07/2023] Open
Abstract
Urbanisation is a major anthropogenic perturbation presenting novel ecological and evolutionary challenges to wild populations. Symbiotic microorganisms residing in the gastrointestinal tracts (gut) of vertebrates have mutual connections with host physiology and respond quickly to environmental alterations. However, the impact of anthropogenic changes and urbanisation on the gut microbiota remains poorly understood, especially in early development. To address this knowledge gap, we characterised the gut microbiota of juvenile great tits (Parus major) reared in artificial nestboxes and in natural cavities in an urban mosaic, employing two distinct frameworks characterising the urban space. Microbial diversity was influenced by cavity type. Alpha diversity was affected by the amount of impervious surface surrounding the breeding location, and positively correlated with tree cover density. Community composition differed between urban and rural sites: these alterations covaried with sound pollution and distance to the city centre. Overall, the microbial communities reflect and are possibly influenced by the heterogeneous environmental modifications that are typical of the urban space. Strikingly, the choice of framework and environmental variables characterising the urban space can influence the outcomes of such ecological studies. Our results open new perspectives to investigate the impact of microbial symbionts on the adaptive capacity of their hosts.
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Affiliation(s)
- Öncü Maraci
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33619, Bielefeld, Germany.
| | - Michela Corsini
- Centre of New Technologies, University of Warsaw, Banacha Street 2C, 02-097, Warsaw, Poland
| | - Anna Antonatou-Papaioannou
- Evolutionary Biology, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
- Institute of Biology-Zoology, Freie Universität Berlin, Köning-Luise-Str. 1-3, 14195, Berlin, Germany
| | - Sebastian Jünemann
- Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615, Bielefeld, Germany
| | - Joanna Sudyka
- Centre of New Technologies, University of Warsaw, Banacha Street 2C, 02-097, Warsaw, Poland
- Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Irene Di Lecce
- Centre of New Technologies, University of Warsaw, Banacha Street 2C, 02-097, Warsaw, Poland
| | - Barbara A Caspers
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33619, Bielefeld, Germany
| | - Marta Szulkin
- Centre of New Technologies, University of Warsaw, Banacha Street 2C, 02-097, Warsaw, Poland
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21
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Worsley SF, Davies CS, Mannarelli ME, Hutchings MI, Komdeur J, Burke T, Dugdale HL, Richardson DS. Gut microbiome composition, not alpha diversity, is associated with survival in a natural vertebrate population. Anim Microbiome 2021; 3:84. [PMID: 34930493 PMCID: PMC8685825 DOI: 10.1186/s42523-021-00149-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/28/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The vertebrate gut microbiome (GM) can vary substantially across individuals within the same natural population. Although there is evidence linking the GM to health in captive animals, very little is known about the consequences of GM variation for host fitness in the wild. Here, we explore the relationship between faecal microbiome diversity, body condition, and survival using data from the long-term study of a discrete natural population of the Seychelles warbler (Acrocephalus sechellensis) on Cousin Island. To our knowledge, this is the first time that GM differences associated with survival have been fully characterised for a natural vertebrate species, across multiple age groups and breeding seasons. RESULTS We identified substantial variation in GM community structure among sampled individuals, which was partially explained by breeding season (5% of the variance), and host age class (up to 1% of the variance). We also identified significant differences in GM community membership between adult birds that survived, versus those that had died by the following breeding season. Individuals that died carried increased abundances of taxa that are known to be opportunistic pathogens, including several ASVs in the genus Mycobacterium. However, there was no association between GM alpha diversity (the diversity of bacterial taxa within a sample) and survival to the next breeding season, or with individual body condition. Additionally, we found no association between GM community membership and individual body condition. CONCLUSIONS These results demonstrate that components of the vertebrate GM can be associated with host fitness in the wild. However, further research is needed to establish whether changes in bacterial abundance contribute to, or are only correlated with, differential survival; this will add to our understanding of the importance of the GM in the evolution of host species living in natural populations.
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Affiliation(s)
- Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
| | - Charli S Davies
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Maria-Elena Mannarelli
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Matthew I Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Terry Burke
- Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield, Sheffield, S10 2TN, UK
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
- Nature Seychelles, Roche Caiman, Mahé, Republic of Seychelles.
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22
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Stothart MR, Newman AEM. Shades of grey: host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal. Anim Microbiome 2021; 3:46. [PMID: 34225812 PMCID: PMC8256534 DOI: 10.1186/s42523-021-00105-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/31/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization (across three cities) on the microbiome of eastern grey squirrels (Sciurus carolinensis). Grey squirrels are ubiquitous in rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate). RESULTS Grey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). The bacterial genera characterizing the microbiomes of built-environment squirrels are thought to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built-environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic expectations. CONCLUSIONS Squirrel microbiomes differed between city and rural environments, but differences of comparable magnitude were observed between land classes at a within-city scale. We did not observe strong evidence that inter-environmental differences were the result of disparate selective pressures. Rather, our results suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. However, these processes were partly mediated by squirrel coat colour phenotype. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide a useful free-living system with which to study how host genetics mediate environment x microbiome interactions.
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Affiliation(s)
- Mason R. Stothart
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, T2N 4Z6 Canada
| | - Amy E. M. Newman
- Department of Integrative Biology, College of Biological Sciences, University of Guelph, Guelph, N1G 2W1 Canada
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23
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Grieves LA, Gloor GB, Kelly TR, Bernards MA, MacDougall-Shackleton EA. Preen gland microbiota of songbirds differ across populations but not sexes. J Anim Ecol 2021; 90:2202-2212. [PMID: 34002375 DOI: 10.1111/1365-2656.13531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/15/2021] [Indexed: 12/30/2022]
Abstract
Metabolites produced by symbiotic microbes can affect the odour of their hosts, providing olfactory cues of identity, sex or other salient features. In birds, preen oil is a major source of body odour that differs between populations and sexes. We hypothesized that population and sex differences in preen oil chemistry reflect underlying differences in preen gland microbiota, predicting that these microbes also differ among populations and between the sexes. We further predicted that pairwise similarity in the community composition of preen gland microbiota would covary with that of preen oil chemical composition, consistent with the fermentation hypothesis for chemical recognition. We analysed preen oil chemistry and preen gland bacterial communities of song sparrows Melospiza melodia. Birds were sampled at sites for which population and sex differences in preen oil have been reported, and at a third site that has been less studied. Consistent with prior work in this system, we found population and sex differences in preen oil chemistry. By contrast, we found population differences but not sex differences in the community composition of preen gland microbes. Overall similarity in the community composition of preen gland microbiota did not significantly covary with that of preen oil chemistry. However, we identified a subset of six microbial genera that maximally correlated with preen oil composition. Although both preen gland microbiota and preen oil composition differ across populations, we did not observe an overall association between them that would implicate symbiotic microbes in mediating variation in olfactory cues associated with preen oil. Instead, certain subsets of microbes may be involved in mediating olfactory cues in birds, but experiments are required to test this.
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Affiliation(s)
| | - Gregory B Gloor
- Biochemistry, University of Western Ontario, London, ON, Canada
| | - Tosha R Kelly
- Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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Sottas C, Schmiedová L, Kreisinger J, Albrecht T, Reif J, Osiejuk TS, Reifová R. Gut microbiota in two recently diverged passerine species: evaluating the effects of species identity, habitat use and geographic distance. BMC Ecol Evol 2021; 21:41. [PMID: 33691625 PMCID: PMC7948333 DOI: 10.1186/s12862-021-01773-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/01/2021] [Indexed: 01/01/2023] Open
Abstract
Background It has been proposed that divergence in the gut microbiota composition between incipient species could contribute to their reproductive isolation. Nevertheless, empirical evidence for the role of gut microbiota in speciation is scarce. Moreover, it is still largely unknown to what extent closely related species in the early stages of speciation differ in their gut microbiota composition, especially in non-mammalian taxa, and which factors drive the divergence. Here we analysed the gut microbiota in two closely related passerine species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (Luscinia luscinia). The ranges of these two species overlap in a secondary contact zone, where both species occasionally hybridize and where interspecific competition has resulted in habitat use differentiation. Results We analysed the gut microbiota from the proximal, middle and distal part of the small intestine in both sympatric and allopatric populations of the two nightingale species using sequencing of bacterial 16S rRNA. We found small but significant differences in the microbiota composition among the three gut sections. However, the gut microbiota composition in the two nightingale species did not differ significantly between either sympatric or allopatric populations. Most of the observed variation in the gut microbiota composition was explained by inter-individual differences. Conclusions To our knowledge, this is the first attempt to assess the potential role of the gut microbiota in bird speciation. Our results suggest that neither habitat use, nor geographical distance, nor species identity have strong influence on the nightingale gut microbiota composition. This suggests that changes in the gut microbiota composition are unlikely to contribute to reproductive isolation in these passerine birds. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01773-1.
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Affiliation(s)
- Camille Sottas
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.
| | - Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, Brno, 603 65, Czech Republic
| | - Jiří Reif
- Faculty of Science, Institute for Environmental Studies, Charles University, Prague, Czech Republic.,Department of Zoology and Laboratory of Ornithology, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Tomasz S Osiejuk
- Department of Behavioural Ecology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
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25
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Locally adapted gut microbiomes mediate host stress tolerance. ISME JOURNAL 2021; 15:2401-2414. [PMID: 33658622 PMCID: PMC8319338 DOI: 10.1038/s41396-021-00940-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/29/2021] [Accepted: 02/11/2021] [Indexed: 01/04/2023]
Abstract
While evidence for the role of the microbiome in shaping host stress tolerance is becoming well-established, to what extent this depends on the interaction between the host and its local microbiome is less clear. Therefore, we investigated whether locally adapted gut microbiomes affect host stress tolerance. In the water flea Daphnia magna, we studied if the host performs better when receiving a microbiome from their source region than from another region when facing a stressful condition, more in particular exposure to the toxic cyanobacteria Microcystis aeruginosa. Therefore, a reciprocal transplant experiment was performed in which recipient, germ-free D. magna, isolated from different ponds, received a donor microbiome from sympatric or allopatric D. magna that were pre-exposed to toxic cyanobacteria or not. We tested for effects on host life history traits and gut microbiome composition. Our data indicate that Daphnia interact with particular microbial strains mediating local adaptation in host stress tolerance. Most recipient D. magna individuals performed better when inoculated with sympatric than with allopatric microbiomes. This effect was most pronounced when the donors were pre-exposed to the toxic cyanobacteria, but this effect was also pond and genotype dependent. We discuss how this host fitness benefit is associated with microbiome diversity patterns.
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Bodawatta KH, Freiberga I, Puzejova K, Sam K, Poulsen M, Jønsson KA. Flexibility and resilience of great tit (Parus major) gut microbiomes to changing diets. Anim Microbiome 2021; 3:20. [PMID: 33602335 PMCID: PMC7893775 DOI: 10.1186/s42523-021-00076-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/12/2021] [Indexed: 12/13/2022] Open
Abstract
Background Gut microbial communities play important roles in nutrient management and can change in response to host diets. The extent of this flexibility and the concomitant resilience is largely unknown in wild animals. To untangle the dynamics of avian-gut microbiome symbiosis associated with diet changes, we exposed Parus major (Great tits) fed with a standard diet (seeds and mealworms) to either a mixed (seeds, mealworms and fruits), a seed, or a mealworm diet for 4 weeks, and examined the flexibility of gut microbiomes to these compositionally different diets. To assess microbiome resilience (recovery potential), all individuals were subsequently reversed to a standard diet for another 4 weeks. Cloacal microbiomes were collected weekly and characterised through sequencing the v4 region of the 16S rRNA gene using Illumina MiSeq. Results Initial microbiomes changed significantly with the diet manipulation, but the communities did not differ significantly between the three diet groups (mixed, seed and mealworm), despite multiple diet-specific changes in certain bacterial genera. Reverting birds to the standard diet led only to a partial recovery in gut community compositions. The majority of the bacterial taxa that increased significantly during diet manipulation decreased in relative abundance after reversion to the standard diet; however, bacterial taxa that decreased during the manipulation rarely increased after diet reversal Conclusions The gut microbial response and partial resilience to dietary changes support that gut bacterial communities of P. major play a role in accommodating dietary changes experienced by wild avian hosts. This may be a contributing factor to the relaxed association between microbiome composition and the bird phylogeny. Our findings further imply that interpretations of wild bird gut microbiome analyses from single-time point sampling, especially for omnivorous species or species with seasonally changing diets, should be done with caution. The partial community recovery implies that ecologically relevant diet changes (e.g., seasonality and migration) open up gut niches that may be filled by previously abundant microbes or replaced by different symbiont lineages, which has important implications for the integrity and specificity of long-term avian-symbiont associations. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00076-6.
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Affiliation(s)
- Kasun H Bodawatta
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Inga Freiberga
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic
| | - Katerina Puzejova
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Katerina Sam
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, Ceske Budejovice, Czech Republic.,Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Knud A Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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27
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Spotswood EN, Beller EE, Grossinger R, Grenier JL, Heller NE, Aronson MFJ. The Biological Deserts Fallacy: Cities in Their Landscapes Contribute More than We Think to Regional Biodiversity. Bioscience 2021; 71:148-160. [PMID: 33613128 PMCID: PMC7882369 DOI: 10.1093/biosci/biaa155] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Cities are both embedded within and ecologically linked to their surrounding landscapes. Although urbanization poses a substantial threat to biodiversity, cities also support many species, some of which have larger populations, faster growth rates, and higher productivity in cities than outside of them. Despite this fact, surprisingly little attention has been paid to the potentially beneficial links between cities and their surroundings. We identify five pathways by which cities can benefit regional ecosystems by releasing species from threats in the larger landscape, increasing regional habitat heterogeneity and genetic diversity, acting as migratory stopovers, preadapting species to climate change, and enhancing public engagement and environmental stewardship. Increasing recognition of these pathways could help cities identify effective strategies for supporting regional biodiversity conservation and could provide a science-based platform for incorporating biodiversity alongside other urban greening goals.
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Affiliation(s)
| | - Erin E Beller
- San Francisco Estuary Institute San Francisco, California in the United States. Erin E. Beller is the Urban Ecology Program manager for the Real Estate and Workplace Services Sustainability Team at Google, Mountain View, California, in the United States
| | - Robin Grossinger
- San Francisco Estuary Institute San Francisco, California in the United States. Erin E. Beller is the Urban Ecology Program manager for the Real Estate and Workplace Services Sustainability Team at Google, Mountain View, California, in the United States
| | - J Letitia Grenier
- San Francisco Estuary Institute San Francisco, California in the United States. Erin E. Beller is the Urban Ecology Program manager for the Real Estate and Workplace Services Sustainability Team at Google, Mountain View, California, in the United States
| | - Nicole E Heller
- Carnegie Museum of Natural History, Pittsburgh, Pennsylvania, United States
| | - Myla F J Aronson
- Department of Ecology, Evolution, and Natural Resources, The State University of New Jersey, New Brunswick, New Jersey, United States
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28
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Herder EA, Spence AR, Tingley MW, Hird SM. Elevation Correlates With Significant Changes in Relative Abundance in Hummingbird Fecal Microbiota, but Composition Changes Little. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.597756] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The microbial communities living on and in vertebrate hosts have myriad effects on their hosts, potentially including fitness and speciation. Microbiomes are influenced by both intrinsic (from the host) and extrinsic (from the environment) factors, but the relative contributions of each are unknown for most non-model species. Abiotic environmental factors can influence the microbiome directly but it is less clear how abiotic gradients shape microbiome communities in the wild. Here, we captured eight wild Anna’s hummingbirds from three different elevations along their elevational distribution in California and moved them directly to a middle (“Within Range”) elevation. After some time at this elevation, the birds were moved in captivity to an “Above Range” elevation, and two birds were later moved back to the Within Range elevation. Fecal and food samples were collected longitudinally and the V4 region of the 16S rRNA gene analyzed. The most abundant phyla in all samples were Fusobacteria, Firmicutes, Actinobacteria, and Proteobacteria. Individual Bird ID explained the greatest amount of microbiome variation at 27.5%, signifying some amount of stability in the Anna’s hummingbird fecal microbiome. Sample elevation explained 19.6% (p = 0.001) of the variation using weighted UniFrac, but only 2.0% (p = 0.047) using unweighted UniFrac, implying a change in abundance of bacterial lineages in the microbiome but not in the presence or absence of the microbes. Additionally, Fusobacteria were 7.0x more abundant in the Above Range elevation samples while Firmicutes were 0.3x lower. A thorough understanding of how the environment can shape the microbiome may assist in conservation efforts and a general understanding of host-microbiome relationships in an era of rapid and global environmental change.
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Berlow M, Phillips JN, Derryberry EP. Effects of Urbanization and Landscape on Gut Microbiomes in White-Crowned Sparrows. MICROBIAL ECOLOGY 2021; 81:253-266. [PMID: 32803364 DOI: 10.1007/s00248-020-01569-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/28/2020] [Indexed: 06/11/2023]
Abstract
Habitats are changing rapidly around the globe and urbanization is one of the primary drivers. Urbanization changes food availability, environmental stressors, and the prevalence of disease for many species. These changes can lead to divergence in phenotypic traits, including behavioral, physiological, and morphological features between urban and rural populations. Recent research highlights that urbanization is also changing the gut microbial communities found in a diverse group of host species. These changes have not been uniform, leaving uncertainty as to how urban habitats are shaping gut microbial communities. To better understand these effects, we investigated the gut bacterial communities of White-Crowned Sparrow (Zonotrichia leucophrys) populations along an urbanization gradient in the San Francisco Bay area. We examined how gut bacterial communities vary with the local environment and host morphological characteristics. We found direct effects of environmental factors, including urban noise levels and territory land cover, as well as indirect effects through body size and condition, on alpha and beta diversity of gut microbial communities. We also found that urban and rural birds' microbiomes differed in which variables predicted their diversity, with urban communities driven by host morphology, and rural communities driven by environmental factors. Elucidating these effects provides a better understanding of how urbanization affects wild avian physiology.
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Affiliation(s)
- Mae Berlow
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA.
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA.
| | - Jennifer N Phillips
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
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30
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Phillips JN, Cooper WJ, Luther DA, Derryberry EP. Territory Quality Predicts Avian Vocal Performance Across an Urban-Rural Gradient. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.587120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human activity around the globe is a growing source of selection pressure on animal behavior and communication systems. Some animals can modify their vocalizations to avoid masking from anthropogenic noise. However, such modifications can also affect the salience of these vocalizations in functional contexts such as competition and mate choice. Such is the case in the well-studied Nuttall's white-crowned sparrow (Zonotrichia leucophrys nuttalli), which lives year-round in both urban San Francisco and nearby rural Point Reyes. A performance feature of this species' song is salient in territorial defense, such that higher performance songs elicit stronger responses in simulated territorial intrusions; but songs with lower performance values transmit better in anthropogenic noise. A key question then is whether vocal performance signals male quality and ability to obtain high quality territories in urban populations. We predicted white-crowned sparrows with higher vocal performance will be in better condition and will tend to hold territories with lower noise levels and more species-preferred landscape features. Because white-crowned sparrows are adapted to coastal scrub habitats, we expect high quality territories to contain lower and less dense canopies, less drought, more greenness, and more flat open ground for foraging. To test our predictions, we recorded songs and measured vocal performance and body condition (scaled mass index and fat score) for a set of urban and rural birds (N = 93), as well as ambient noise levels on their territories. Remote sensing metrics measured landscape features of territories, such as drought stress (NDWI), greenness (NDVI), mean canopy height, maximum height, leaf area density (understory and canopy), slope, and percent bare ground for a 50 m radius on each male territory. We did not find a correlation between body condition and performance but did find a relationship between noise levels and performance. Further, high performers held territories with lower canopies and less dense vegetation, which are species-preferred landscape features. These findings link together fundamental aspects of sexual selection in that habitat quality and the quality of sexually selected signals appear to be associated: males that have the highest performing songs are defending territories of the highest quality.
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31
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An altered microbiome in urban coyotes mediates relationships between anthropogenic diet and poor health. Sci Rep 2020; 10:22207. [PMID: 33335116 PMCID: PMC7746695 DOI: 10.1038/s41598-020-78891-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022] Open
Abstract
Generalist species able to exploit anthropogenic food sources are becoming increasingly common in urban environments. Coyotes (Canis latrans) are one such urban generalist that now resides in cities across North America, where diseased or unhealthy coyotes are frequently reported in cases of human-wildlife conflict. Coyote health and fitness may be related to habitat use and diet via the gut microbiome, which has far-reaching effects on animal nutrition and physiology. In this study, we used stomach contents, stable isotope analysis, 16S rRNA gene amplicon sequencing, and measures of body condition to identify relationships among habitat use, diet, fecal microbiome composition, and health in urban and rural coyotes. Three distinct relationships emerged: (1) Urban coyotes consumed more anthropogenic food, which was associated with increased microbiome diversity, higher abundances of Streptococcus and Enterococcus, and poorer average body condition. (2) Conversely, rural coyotes harbored microbiomes rich in Fusobacteria, Sutterella, and Anaerobiospirillum, which were associated with protein-rich diets and improved body condition. (3) Diets rich in anthropogenic food were associated with increased abundances of Erysipelotrichiaceae, Lachnospiraceae, and Coriobacteriaceae, which correlated with larger spleens in urban coyotes. Urban coyotes also had an increased prevalence of the zoonotic parasite Echinococcus multilocularis, but there were no detectable connections between parasite infection and microbiome composition. Our results demonstrate how the consumption of carbohydrate-rich anthropogenic food by urban coyotes alters the microbiome to negatively affect body condition, with potential relationships to parasite susceptibility and conflict-prone behavior.
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32
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Davidson GL, Wiley N, Cooke AC, Johnson CN, Fouhy F, Reichert MS, de la Hera I, Crane JMS, Kulahci IG, Ross RP, Stanton C, Quinn JL. Diet induces parallel changes to the gut microbiota and problem solving performance in a wild bird. Sci Rep 2020; 10:20783. [PMID: 33247162 PMCID: PMC7699645 DOI: 10.1038/s41598-020-77256-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
The microbial community in the gut is influenced by environmental factors, especially diet, which can moderate host behaviour through the microbiome-gut-brain axis. However, the ecological relevance of microbiome-mediated behavioural plasticity in wild animals is unknown. We presented wild-caught great tits (Parus major) with a problem-solving task and showed that performance was weakly associated with variation in the gut microbiome. We then manipulated the gut microbiome by feeding birds one of two diets that differed in their relative levels of fat, protein and fibre content: an insect diet (low content), or a seed diet (high content). Microbial communities were less diverse among individuals given the insect compared to those on the seed diet. Individuals were less likely to problem-solve after being given the insect diet, and the same microbiota metrics that were altered as a consequence of diet were also those that correlated with variation in problem solving performance. Although the effect on problem-solving behaviour could have been caused by motivational or nutritional differences between our treatments, our results nevertheless raise the possibility that dietary induced changes in the gut microbiota could be an important mechanism underlying individual behavioural plasticity in wild populations.
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Affiliation(s)
- Gabrielle L Davidson
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, Ireland.
- Department of Psychology, Downing Street, University of Cambridge, Cambridge, UK.
| | - Niamh Wiley
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Amy C Cooke
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, Ireland
| | - Crystal N Johnson
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Fiona Fouhy
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Michael S Reichert
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, Ireland
- Department of Integrative Biology, Oklahoma State University, Stillwater, USA
| | - Iván de la Hera
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, Ireland
- Department of Integrative Biology, Oklahoma State University, Stillwater, USA
| | - Jodie M S Crane
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, Ireland
- Kākāpō Recovery Programme, Department of Conservation, 7th Floor, 33 Don Street, Invercargill, 9810, New Zealand
| | - Ipek G Kulahci
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, Ireland
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Science Center, Notre Dame, IN, 46556, USA
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - John L Quinn
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, Ireland.
- Environmental Research Institute, University College Cork, Cork, Ireland.
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Derryberry EP, Phillips JN, Derryberry GE, Blum MJ, Luther D. Singing in a silent spring: Birds respond to a half-century soundscape reversion during the COVID-19 shutdown. Science 2020; 370:575-579. [PMID: 32972991 DOI: 10.1126/science.abd5777] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/09/2020] [Indexed: 12/15/2022]
Abstract
Actions taken to control the coronavirus disease 2019 (COVID-19) pandemic have conspicuously reduced motor vehicle traffic, potentially alleviating auditory pressures on animals that rely on sound for survival and reproduction. Here, by comparing soundscapes and songs across the San Francisco Bay Area before and during the recent statewide shutdown, we evaluated whether a common songbird responsively exploited newly emptied acoustic space. We show that noise levels in urban areas were substantially lower during the shutdown, characteristic of traffic in the mid-1950s. We also show that birds responded by producing higher performance songs at lower amplitudes, effectively maximizing communication distance and salience. These findings illustrate that behavioral traits can change rapidly in response to newly favorable conditions, indicating an inherent resilience to long-standing anthropogenic pressures such as noise pollution.
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Affiliation(s)
- Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA.
| | - Jennifer N Phillips
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA.,Department of Science and Mathematics, Texas A&M University-San Antonio, San Antonio, TX 78224, USA
| | - Graham E Derryberry
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Michael J Blum
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - David Luther
- Department of Biology, George Mason University, Fairfax, VA 22030, USA
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Teyssier A, Matthysen E, Hudin NS, de Neve L, White J, Lens L. Diet contributes to urban-induced alterations in gut microbiota: experimental evidence from a wild passerine. Proc Biol Sci 2020; 287:20192182. [PMID: 32019440 DOI: 10.1098/rspb.2019.2182] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Urban sprawl increasingly affects the ecology of natural populations, including host-microbiota interactions, with observed differences in the gut microbiota between urban and rural hosts. While different mechanisms could explain this pattern, dietary uptake constitutes a likely candidate. To assess the contribution of diet in explaining urban-rural variation in gut microbiota, we performed an aviary experiment in which urban and rural house sparrows were fed with mimics of urban or rural diets. Before the experiment, rural sparrows hosted more diverse gut communities, with a higher relative abundance of Enterococcaceae and Staphylococcaceae and lower abundance of genes involved in xenobiotic degradation and lipid metabolism than their urban counterparts. The experimental diets significantly altered gut microbiota α- and β-diversity and taxonomic composition, with the strongest shifts occurring in individuals exposed to contrasting diets. Overall, diet-induced shifts resembled initial differences between free-ranging urban and rural hosts. Furthermore, rural diet had a positive impact on urban host body mass but only in hosts with the highest initial gut diversity. Overall, our results indicate that diet constitutes an important factor contributing to differences in gut microbiota along the urbanization gradient and provide new insights on possible fitness consequences of a reduced gut diversity in urban settings.
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Affiliation(s)
- Aimeric Teyssier
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.,Evolutionary Ecology Group, Department of Biology, University of Antwerp, Wilrijk, Belgium.,Evolution and Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Erik Matthysen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Noraine Salleh Hudin
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.,Department of Biological Sciences, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900 Tanjong Malim, Perak, Malaysia
| | - Liesbeth de Neve
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Joël White
- Evolution and Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-IRD, 118 route de Narbonne, 31062 Toulouse, France.,ENSFEA, 2 route de Narbonne, 31326 Castanet-Tolosan, France
| | - Luc Lens
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
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Affiliation(s)
| | - Daniel T. Blumstein
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
| | | | - Sasha G. Tetu
- Department of Molecular Sciences Macquarie University North Ryde NSW Australia
| | - Michael R. Gillings
- Department of Biological Sciences Macquarie University North Ryde NSW Australia
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Characteristics of Microbial Communities of Pachygrontha antennata (Hemiptera: Pachygronthidae) in Relation to Habitat Variables. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16234668. [PMID: 31771134 PMCID: PMC6926961 DOI: 10.3390/ijerph16234668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/14/2019] [Accepted: 11/20/2019] [Indexed: 12/26/2022]
Abstract
The microbial community interacts with the environment and the health and immune function of its host both directly and indirectly. However, very few studies about microbial communities have considered habitat and external environmental variables. This study examined environmental influences on the microbial community of Pachygrontha antennata, which is found in various habitats (e.g., urban, forested, and agricultural areas). The results demonstrated that the composition of the microbial community differed according to land use, while the bacterial diversity did not. In urban areas with high environmental heterogeneity, microbial community diversity tended to be high. Furthermore, bacteria in forests and agricultural areas (e.g., Paraburkholderia, Burkholderia) have been found to be highly correlated with habitat variables. Therefore, we suggest that habitat variables should be considered in future symbiotic studies.
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Littleford-Colquhoun BL, Weyrich LS, Kent N, Frere CH. City life alters the gut microbiome and stable isotope profiling of the eastern water dragon (Intellagama lesueurii). Mol Ecol 2019; 28:4592-4607. [PMID: 31495003 DOI: 10.1111/mec.15240] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/09/2019] [Accepted: 08/09/2019] [Indexed: 12/31/2022]
Abstract
Urbanisation is one of the most significant threats to biodiversity, due to the rapid and large-scale environmental alterations it imposes on the natural landscape. It is, therefore, imperative that we understand the consequences of and mechanisms by which, species can respond to it. In recent years, research has shown that plasticity of the gut microbiome may be an important mechanism by which animals can adapt to environmental change, yet empirical evidence of this in wild non-model species remains sparse. Using an empirical replicated study system, we show that city life alters the gut microbiome and stable isotope profiling of a wild native non-model species - the eastern water dragon (Intellagama lesueurii) in Queensland, Australia. City dragons exhibit a more diverse gut microbiome than their native habitat counterparts and show gut microbial signatures of a high fat and plant rich diet. Additionally, we also show that city dragons have elevated levels of the Nitrogen-15 isotope in their blood suggesting that a city diet, which incorporates novel anthropogenic food sources, may also be richer in protein. These results highlight the role that gut microbial plasticity plays in an animals' response to human-altered landscapes.
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Affiliation(s)
- Bethan L Littleford-Colquhoun
- Global Change Ecology Research Group, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Qld, Australia
| | - Laura S Weyrich
- Department of Genetics and Evolution, Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA, Australia.,Centre for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, NSW, Australia
| | - Nicola Kent
- Global Change Ecology Research Group, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Qld, Australia
| | - Celine H Frere
- Global Change Ecology Research Group, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Qld, Australia
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38
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Knutie SA, Chaves JA, Gotanda KM. Human activity can influence the gut microbiota of Darwin's finches in the Galapagos Islands. Mol Ecol 2019; 28:2441-2450. [DOI: 10.1111/mec.15088] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/21/2019] [Accepted: 03/22/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Sarah A. Knutie
- Department of Ecology and Evolutionary Biology University of Connecticut Storrs Connecticut
| | - Jaime A. Chaves
- Colegio de Ciencias Biológicas y Ambientales Universidad San Francisco de Quito Cumbayá Quito Ecuador
- Galápagos Science Center Puerto Baquerizo Moreno Ecuador
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