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Mei C, Shi Y, Wang Y, Qiu Z, Yang H. Termitidicoccus mucosus gen. nov. sp. nov. a novel Verrucomicrobiota species isolated from Reticulitermes chinensis gives insights of high adaptability of symbiotic bacteria to termite gut ecosystem. Res Microbiol 2024; 175:104173. [PMID: 38157920 DOI: 10.1016/j.resmic.2023.104173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 10/27/2023] [Accepted: 12/07/2023] [Indexed: 01/03/2024]
Abstract
Verrucomicrobiota is widely distributed in various habitats including insect guts. It was found to be prevalent in almost all investigated termite guts, whereas their physiological functions are not very clear. In this study we characterized the physiological and genomic properties of Verrucomicrobiota strain TSB47T isolated from Reticulitermes chinensis. The cells of strain TSB47T were Gram-stain-negative, non-motile, and non-spore-forming coccoid with one or more warts. 16S rRNA gene analysis showed that the closest relatives of strain TSB47T were Opitutaceae strain TAV1 and Ereboglobus luteus Ho45T (98.3% and 95.4% sequence similarity, respectively). Whole genome analysis revealed that there are a large number of glycoside hydrolase genes, amino acid metabolism genes, complete Mo-Fe nitrogenase and Fe-Fe nitrogenase gene clusters, as well as cbb3-type cytochrome oxidase gene in the genome of strain TSB47T. Strain TSB47T grows well under anaerobic and microaerophilic conditions with a strong tolerance to oxygen. Physiological and genomic characters of strain TSB47T indicated its high adaptability to termite gut ecosystem. Based on phenotypic and phylogenetic evidence, we suggest strain TSB47T as the type species of a novel genus in the family Opitutaceae, for which the name Termitidicoccus mucosus sp. nov. is proposed. The type strain is TSB47T (CCTCC AB2022447T; KCTC 102044T).
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Affiliation(s)
- Cheng Mei
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Yu Shi
- College of Food and Biotechnology, Wuhan Institute of Design and Sciences, Wuhan 430079, PR China
| | - Yu Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Zhengyong Qiu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Hong Yang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.
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Yan H, Wang E, Wei GS, Zhang B, Xu X. Both host and diet shape bacterial communities of predatory mites. INSECT SCIENCE 2024; 31:551-561. [PMID: 37469127 DOI: 10.1111/1744-7917.13253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/23/2023] [Accepted: 06/09/2023] [Indexed: 07/21/2023]
Abstract
Microbial communities, derived from food, ambient, and inner, can affect host ecological adaption and evolution. Comparing with most phytophagous arthropods, predators may have more opportunities to develop specific microbiota depending on the level of prey specialization. To explore how diet sources affect host microbial communities and vary across predator species, we considered 3 types of predators from Phytoseiidae (Acari: Mesostigmata): polyphagous (Amblyseius orientalis Ehara, Neoseiulus barkeri Hughes, and Amblyseius swirskii Athias-Henrio), oligophagous (Neoseiulus californicus McGregor), and monophagous (Phytoseiulus persimilis Athias-Henriot) predatory mites. The polyphagous species were fed on 2 types of diets, natural prey and alternative prey. By using 16S rRNA sequencing, we found that diet was the main source of microbiota in predatory mites, while there was no clear pattern affected by prey specialization. Among 3 polyphagous predators, host species had a larger impact than prey on microbial composition. Unlike A. orientalis or N. barkeri which showed consistency in their microbiota, prey switching significantly affected β-diversity of bacterial composition in A. swirskii, with 56% of the microbial alteration. In short, our results confirmed the substantial influence of diet on host microbial construction in predatory species, and highlighted species differences in shaping the microbiota which are not necessarily related to prey specialization.
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Affiliation(s)
- Hong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei Province, China
| | - Endong Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guo-Shu Wei
- College of Plant Protection, Hebei Agricultural University, Baoding, Hebei Province, China
| | - Bo Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Xuenong Xu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Beijing, China
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3
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Valdivia C, Newton JA, von Beeren C, O'Donnell S, Kronauer DJC, Russell JA, Łukasik P. Microbial symbionts are shared between ants and their associated beetles. Environ Microbiol 2023; 25:3466-3483. [PMID: 37968789 DOI: 10.1111/1462-2920.16544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023]
Abstract
The transmission of microbial symbionts across animal species could strongly affect their biology and evolution, but our understanding of transmission patterns and dynamics is limited. Army ants (Formicidae: Dorylinae) and their hundreds of closely associated insect guest species (myrmecophiles) can provide unique insights into interspecific microbial symbiont sharing. Here, we compared the microbiota of workers and larvae of the army ant Eciton burchellii with those of 13 myrmecophile beetle species using 16S rRNA amplicon sequencing. We found that the previously characterized specialized bacterial symbionts of army ant workers were largely absent from ant larvae and myrmecophiles, whose microbial communities were usually dominated by Rickettsia, Wolbachia, Rickettsiella and/or Weissella. Strikingly, different species of myrmecophiles and ant larvae often shared identical 16S rRNA genotypes of these common bacteria. Protein-coding gene sequences confirmed the close relationship of Weissella strains colonizing army ant larvae, some workers and several myrmecophile species. Unexpectedly, these strains were also similar to strains infecting dissimilar animals inhabiting very different habitats: trout and whales. Together, our data show that closely interacting species can share much of their microbiota, and some versatile microbial species can inhabit and possibly transmit across a diverse range of hosts and environments.
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Affiliation(s)
- Catalina Valdivia
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Justin A Newton
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Christoph von Beeren
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, New York, USA
| | - Sean O'Donnell
- Department of Biodiversity, Earth & Environmental Science, Drexel University, Philadelphia, Pennsylvania, USA
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, New York, New York, USA
| | - Jacob A Russell
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
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Nepel M, Mayer VE, Barrajon-Santos V, Woebken D. Bacterial diversity in arboreal ant nesting spaces is linked to colony developmental stage. Commun Biol 2023; 6:1217. [PMID: 38036598 PMCID: PMC10689775 DOI: 10.1038/s42003-023-05577-5] [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: 03/30/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023] Open
Abstract
The omnipresence of ants is commonly attributed to their eusocial organization and division of labor, however, bacteria in their nests may facilitate their success. Like many other arboreal ants living in plant-provided cavities, Azteca ants form dark-colored "patches" in their nesting space inside Cecropia host plants. These patches are inhabited by bacteria, fungi and nematodes and appear to be essential for ant colony development. Yet, detailed knowledge of the microbial community composition and its consistency throughout the life cycle of ant colonies was lacking. Amplicon sequencing of the microbial 16S rRNA genes in patches from established ant colonies reveals a highly diverse, ant species-specific bacterial community and little variation within an individual ant colony, with Burkholderiales, Rhizobiales and Chitinophagales being most abundant. In contrast, bacterial communities of early ant colony stages show low alpha diversity and no ant species-specific community composition. We suggest a substrate-caused bottleneck after vertical transmission of the bacterial patch community from mother to daughter colonies. The subsequent ecological succession is driven by environmental parameters and influenced by ant behavior. Our study provides key information for future investigations determining the functions of these bacteria, which is essential to understand the ubiquity of such patches among arboreal ants.
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Affiliation(s)
- Maximilian Nepel
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria.
| | - Veronika E Mayer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.
| | - Veronica Barrajon-Santos
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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Hettiarachchi A, Cnockaert M, Joossens M, Laureys D, De Clippeleer J, Vereecken NJ, Michez D, Smagghe G, de Graaf DC, Vandamme P. Convivina is a specialised core gut symbiont of the invasive hornet Vespa velutina. INSECT MOLECULAR BIOLOGY 2023; 32:510-527. [PMID: 37204105 DOI: 10.1111/imb.12847] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/28/2023] [Indexed: 05/20/2023]
Abstract
We provide a culturomics analysis of the cultivable bacterial communities of the crop, midgut and hindgut compartments, as well as the ovaries, of the invasive insect Vespa velutina, along with a cultivation-independent analysis of samples of the same nest through 16S rRNA amplicon sequencing. The Vespa velutina bacterial symbiont community was dominated by the genera Convivina, Fructobacillus, Lactiplantibacillus, Lactococcus, Sphingomonas and Spiroplasma. Lactococcus lactis and Lactiplantibacillus plantarum represented generalist core lactic acid bacteria (LAB) symbionts, while Convivina species and Fructobacillus fructosus represented highly specialised core LAB symbionts with strongly reduced genome sizes. Sphingomonas and Spiroplasma were the only non-LAB core symbionts but were not isolated. Convivina bacteria were particularly enriched in the hornet crop and included Convivina intestini, a species adapted towards amino acid metabolism, and Convivina praedatoris sp. nov. which was adapted towards carbohydrate metabolism.
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Affiliation(s)
- Amanda Hettiarachchi
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Marie Joossens
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - David Laureys
- Innovation Centre for Brewing & Fermentation, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jessika De Clippeleer
- Innovation Centre for Brewing & Fermentation, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | - Denis Michez
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Dirk C de Graaf
- Laboratory of Molecular Entomology and Bee Pathology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
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Béchade B, Cabuslay CS, Hu Y, Mendonca CM, Hassanpour B, Lin JY, Su Y, Fiers VJ, Anandarajan D, Lu R, Olson CJ, Duplais C, Rosen GL, Moreau CS, Aristilde L, Wertz JT, Russell JA. Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants. THE ISME JOURNAL 2023; 17:1751-1764. [PMID: 37558860 PMCID: PMC10504363 DOI: 10.1038/s41396-023-01490-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023]
Abstract
While genome sequencing has expanded our knowledge of symbiosis, role assignment within multi-species microbiomes remains challenging due to genomic redundancy and the uncertainties of in vivo impacts. We address such questions, here, for a specialized nitrogen (N) recycling microbiome of turtle ants, describing a new genus and species of gut symbiont-Ischyrobacter davidsoniae (Betaproteobacteria: Burkholderiales: Alcaligenaceae)-and its in vivo physiological context. A re-analysis of amplicon sequencing data, with precisely assigned Ischyrobacter reads, revealed a seemingly ubiquitous distribution across the turtle ant genus Cephalotes, suggesting ≥50 million years since domestication. Through new genome sequencing, we also show that divergent I. davidsoniae lineages are conserved in their uricolytic and urea-generating capacities. With phylogenetically refined definitions of Ischyrobacter and separately domesticated Burkholderiales symbionts, our FISH microscopy revealed a distinct niche for I. davidsoniae, with dense populations at the anterior ileum. Being positioned at the site of host N-waste delivery, in vivo metatranscriptomics and metabolomics further implicate I. davidsoniae within a symbiont-autonomous N-recycling pathway. While encoding much of this pathway, I. davidsoniae expressed only a subset of the requisite steps in mature adult workers, including the penultimate step deriving urea from allantoate. The remaining steps were expressed by other specialized gut symbionts. Collectively, this assemblage converts inosine, made from midgut symbionts, into urea and ammonia in the hindgut. With urea supporting host amino acid budgets and cuticle synthesis, and with the ancient nature of other active N-recyclers discovered here, I. davidsoniae emerges as a central player in a conserved and impactful, multipartite symbiosis.
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Affiliation(s)
- Benoît Béchade
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA.
| | - Christian S Cabuslay
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
| | - Yi Hu
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 100875, Beijing, China
| | - Caroll M Mendonca
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, 60208, USA
| | - Bahareh Hassanpour
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, 60208, USA
| | - Jonathan Y Lin
- Department of Biology, Calvin University, 1726 Knollcrest Circle SE, Grand Rapids, MI, 49546-4402, USA
| | - Yangzhou Su
- Department of Biology, Calvin University, 1726 Knollcrest Circle SE, Grand Rapids, MI, 49546-4402, USA
| | - Valerie J Fiers
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
| | - Dharman Anandarajan
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
| | - Richard Lu
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
| | - Chandler J Olson
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
- Department of Biological Sciences, University of Alabama, 1325 Hackberry Ln, Tuscaloosa, AL, 35487, USA
| | - Christophe Duplais
- Department of Entomology, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
| | - Gail L Rosen
- Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Department of Electrical and Computer Engineering, Drexel University, 3141 Chestnut St., Philadelphia, PA, 19104, USA
| | - Corrie S Moreau
- Department of Entomology, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, 60208, USA
| | - John T Wertz
- Department of Biology, Calvin University, 1726 Knollcrest Circle SE, Grand Rapids, MI, 49546-4402, USA
| | - Jacob A Russell
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
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Bacci G, Fratini S, Meriggi N, Cheng CLY, Ng KH, Pindo M, Iannucci A, Mengoni A, Cavalieri D, Cannicci S. Conserved organ-specific microbial assemblages in different populations of a terrestrial crab. Front Microbiol 2023; 14:1113617. [PMID: 37378290 PMCID: PMC10291174 DOI: 10.3389/fmicb.2023.1113617] [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: 12/01/2022] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Microorganisms are ubiquitous in the environment and provide genetic and physiological functions to multicellular organisms. Knowledge on the associated microbiota is becoming highly relevant to understand the host's ecology and biology. Among invertebrates, many examples of endosymbiosis have been described, such as those in corals, ants, and termites. At present, however, little is known on the presence, diversity, and putative roles of the microbiota associated to brachyuran crabs in relation to their environment. In this work we investigated the associated microbiota of three populations of the terrestrial brachyuran crab Chiromantes haematocheir to find evidence of a conserved organ-specific microbiome unrelated to the population of origin and dissimilar from environmental microbial assemblages. Bacterial 16S rRNA gene and fungal ITS sequences were obtained from selected crab organs and environmental matrices to profile microbial communities. Despite the presence of truly marine larval stages and the absence of a gregarious behaviour, favouring microbiota exchanges, we found common, organ-specific microbiota, associated with the gut and the gills of crabs from the different populations (with more than 15% of the genera detected specifically enriched only in one organ). These findings suggest the presence of possible functional roles of the organ-specific microbiota.
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Affiliation(s)
- Giovanni Bacci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Sara Fratini
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | | | - Ka Hei Ng
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Massimo Pindo
- The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Alessio Iannucci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Duccio Cavalieri
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Stefano Cannicci
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
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Suenami S, Koto A, Miyazaki R. Basic Structures of Gut Bacterial Communities in Eusocial Insects. INSECTS 2023; 14:insects14050444. [PMID: 37233072 DOI: 10.3390/insects14050444] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/28/2023] [Accepted: 05/04/2023] [Indexed: 05/27/2023]
Abstract
Gut bacterial communities assist host animals with numerous functions such as food digestion, nutritional provision, or immunity. Some social mammals and insects are unique in that their gut microbial communities are stable among individuals. In this review, we focus on the gut bacterial communities of eusocial insects, including bees, ants, and termites, to provide an overview of their community structures and to gain insights into any general aspects of their structural basis. Pseudomonadota and Bacillota are prevalent bacterial phyla commonly detected in those three insect groups, but their compositions are distinct at lower taxonomic levels. Eusocial insects harbor unique gut bacterial communities that are shared within host species, while their stability varies depending on host physiology and ecology. Species with narrow dietary habits, such as eusocial bees, harbor highly stable and intraspecific microbial communities, while generalists, such as most ant species, exhibit relatively diverse community structures. Caste differences could influence the relative abundance of community members without significantly altering the taxonomic composition.
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Affiliation(s)
- Shota Suenami
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
| | - Akiko Koto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
- Computational Bio Big Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo 169-8555, Japan
| | - Ryo Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Japan
- Computational Bio Big Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo 169-8555, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
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Xiao Q, Wang L, Chen SQ, Zheng CY, Lu YY, Xu YJ. Gut Microbiome Composition of the Fire Ant Solenopsis invicta: an Integrated Analysis of Host Genotype and Geographical Distribution. Microbiol Spectr 2023; 11:e0358522. [PMID: 36602316 PMCID: PMC9927370 DOI: 10.1128/spectrum.03585-22] [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: 09/06/2022] [Accepted: 12/01/2022] [Indexed: 01/06/2023] Open
Abstract
Gut symbiotic bacteria are known to be closely related to insect development, nutrient metabolism, and disease resistance traits, but the most important factors leading to changes in these communities have not been well clarified. To address this, we examined the associations between the gut symbiotic bacteria and the host genotype and geographical distribution of Solenopsis invicta in China, where it is invasive and has spread primarily by human-mediated dispersal. Thirty-two phyla were detected in the gut symbiotic bacteria of S. invicta. Proteobacteria were the most dominant group among the gut symbiotic bacteria. Furthermore, the Bray-Curtis dissimilarity matrices of the gut symbiotic bacteria were significantly positively correlated with the geographical distance between the host ant colonies, but this relationship was affected by the social form. The distance between monogyne colonies had a significant effect on the Bray-Curtis dissimilarity matrices of gut symbiotic bacteria, but the distance between polygyne colonies did not. Moreover, the Bray-Curtis dissimilarity matrices were positively correlated with Nei's genetic distance of the host but were not correlated with the COI-based genetic distance. This study provides a scientific basis for further understanding the ecological adaptability of red imported fire ants during invasion and dispersal. IMPORTANCE We demonstrated that gut microbiota composition and diversity varied among populations. These among-population differences were associated with host genotype and geographical distribution. Our results suggested that population-level differences in S. invicta gut microbiota may depend more on environmental factors than on host genotype.
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Affiliation(s)
- Qian Xiao
- Red Imported Fire Ant Research Center, South China Agricultural University, Guangzhou, China
| | - Lei Wang
- Red Imported Fire Ant Research Center, South China Agricultural University, Guangzhou, China
| | - Si-Qi Chen
- Red Imported Fire Ant Research Center, South China Agricultural University, Guangzhou, China
| | - Chun-Yan Zheng
- Red Imported Fire Ant Research Center, South China Agricultural University, Guangzhou, China
| | - Yong-Yue Lu
- Red Imported Fire Ant Research Center, South China Agricultural University, Guangzhou, China
| | - Yi-Juan Xu
- Red Imported Fire Ant Research Center, South China Agricultural University, Guangzhou, China
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Jackson R, Patapiou PA, Golding G, Helanterä H, Economou CK, Chapuisat M, Henry LM. Evidence of phylosymbiosis in Formica ants. Front Microbiol 2023; 14:1044286. [PMID: 37213490 PMCID: PMC10196114 DOI: 10.3389/fmicb.2023.1044286] [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: 09/14/2022] [Accepted: 03/31/2023] [Indexed: 05/23/2023] Open
Abstract
Introduction Insects share intimate relationships with microbes that play important roles in their biology. Yet our understanding of how host-bound microbial communities assemble and perpetuate over evolutionary time is limited. Ants host a wide range of microbes with diverse functions and are an emerging model for studying the evolution of insect microbiomes. Here, we ask whether phylogenetically related ant species have formed distinct and stable microbiomes. Methods To answer this question, we investigated the microbial communities associated with queens of 14 Formica species from five clades, using deep coverage 16S rRNA amplicon sequencing. Results We reveal that Formica species and clades harbor highly defined microbial communities that are dominated by four bacteria genera: Wolbachia, Lactobacillus, Liliensternia, and Spiroplasma. Our analysis reveals that the composition of Formica microbiomes mirrors the phylogeny of the host, i.e., phylosymbiosis, in that related hosts harbor more similar microbial communities. In addition, we find there are significant correlations between microbe co-occurrences. Discussion Our results demonstrate Formica ants carry microbial communities that recapitulate the phylogeny of their hosts. Our data suggests that the co-occurrence of different bacteria genera may at least in part be due to synergistic and antagonistic interactions between microbes. Additional factors potentially contributing to the phylosymbiotic signal are discussed, including host phylogenetic relatedness, host-microbe genetic compatibility, modes of transmission, and similarities in host ecologies (e.g., diets). Overall, our results support the growing body of evidence that microbial community composition closely depends on the phylogeny of their hosts, despite bacteria having diverse modes of transmission and localization within the host.
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Affiliation(s)
- Raphaella Jackson
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Patapios A. Patapiou
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Gemma Golding
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Heikki Helanterä
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
- Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Chloe K. Economou
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Michel Chapuisat
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Lee M. Henry
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
- *Correspondence: Lee M. Henry,
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Ravigné V, Becker N, Massol F, Guichoux E, Boury C, Mahé F, Facon B. Fruit fly phylogeny imprints bacterial gut microbiota. Evol Appl 2022; 15:1621-1638. [PMID: 36330298 PMCID: PMC9624087 DOI: 10.1111/eva.13352] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 11/30/2022] Open
Abstract
One promising avenue for reconciling the goals of crop production and ecosystem preservation consists in the manipulation of beneficial biotic interactions, such as between insects and microbes. Insect gut microbiota can affect host fitness by contributing to development, host immunity, nutrition, or behavior. However, the determinants of gut microbiota composition and structure, including host phylogeny and host ecology, remain poorly known. Here, we used a well-studied community of eight sympatric fruit fly species to test the contributions of fly phylogeny, fly specialization, and fly sampling environment on the composition and structure of bacterial gut microbiota. Comprising both specialists and generalists, these species belong to five genera from to two tribes of the Tephritidae family. For each fly species, one field and one laboratory samples were studied. Bacterial inventories to the genus level were produced using 16S metabarcoding with the Oxford Nanopore Technology. Sample bacterial compositions were analyzed with recent network-based clustering techniques. Whereas gut microbiota were dominated by the Enterobacteriaceae family in all samples, microbial profiles varied across samples, mainly in relation to fly identity and sampling environment. Alpha diversity varied across samples and was higher in the Dacinae tribe than in the Ceratitinae tribe. Network analyses allowed grouping samples according to their microbial profiles. The resulting groups were very congruent with fly phylogeny, with a significant modulation of sampling environment, and with a very low impact of fly specialization. Such a strong imprint of host phylogeny in sympatric fly species, some of which share much of their host plants, suggests important control of fruit flies on their gut microbiota through vertical transmission and/or intense filtering of environmental bacteria.
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Affiliation(s)
- Virginie Ravigné
- CIRADUMR PHIMMontpellierFrance
- PHIMUniv MontpellierCIRADINRAEInstitut AgroIRDMontpellierFrance
| | | | - François Massol
- InsermCHU LilleInstitut Pasteur de LilleU1019 – UMR 9017Center for Infection and Immunity of Lille (CIIL)CNRSUniversité de LilleLilleFrance
| | - Erwan Guichoux
- INRAE ‐ UMR 1202 BIOGECO ‐ Plateforme Genome Transcriptome de BordeauxCestasFrance
| | - Christophe Boury
- INRAE ‐ UMR 1202 BIOGECO ‐ Plateforme Genome Transcriptome de BordeauxCestasFrance
| | - Frédéric Mahé
- CIRADUMR PHIMMontpellierFrance
- PHIMUniv MontpellierCIRADINRAEInstitut AgroIRDMontpellierFrance
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12
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Rocha FP, Ronque MUV, Lyra ML, Bacci M, Oliveira PS. Habitat and Host Species Drive the Structure of Bacterial Communities of Two Neotropical Trap-Jaw Odontomachus Ants : Habitat and Host Species Drive the Structure of Bacterial Communities of Two Neotropical Trap-Jaw Odontomachus Ants. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02064-y. [PMID: 35802173 DOI: 10.1007/s00248-022-02064-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Ants have long been known for their associations with other taxa, including macroscopic fungi and symbiotic bacteria. Recently, many ant species have had the composition and function of their bacterial communities investigated. Due to its behavioral and ecological diversity, the subfamily Ponerinae deserves more attention regarding its associated microbiota. Here, we used the V4 region of the 16S rRNA gene to characterize the bacterial communities of Odontomachus chelifer (ground-nesting) and Odontomachus hastatus (arboreal), two ponerine trap-jaw species commonly found in the Brazilian savanna ("Cerrado") and Atlantic rainforest. We investigated habitat effects (O. chelifer in the Cerrado and the Atlantic rainforest) and species-specific effects (both species in the Atlantic rainforest) on the bacterial communities' structure (composition and abundance) in two different body parts: cuticle and gaster. Bacterial communities differed in all populations studied. Cuticular communities were more diverse, while gaster communities presented variants common to other ants, including Wolbachia and Candidatus Tokpelaia hoelldoblerii. Odontomachus chelifer populations presented different communities in both body parts, highlighting the influence of habitat type. In the Atlantic rainforest, the outcome depended on the body part targeted. Cuticular communities were similar between species, reinforcing the habitat effect on bacterial communities, which are mainly composed of environmentally acquired taxa. Gaster communities, however, differed between the two Odontomachus species, suggesting species-specific effects and selective filters. Unclassified Firmicutes and uncultured Rhizobiales variants are the main components accounting for the observed differences. Our study indicates that both host species and habitat act synergistically, but to different degrees, to shape the bacterial communities in these Odontomachus species.
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Affiliation(s)
- Felipe P Rocha
- Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil
- The University of Hong Kong, Pokfulam Road, Hong Kong Island, SAR, Hong Kong
| | - Mariane U V Ronque
- Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil
- Universidade Estadual do Norte do Paraná, Ciências Biológicas, Cornélio Procópio, PR, Brazil
| | - Mariana L Lyra
- Departamento de Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista - Campus Rio Claro, Rio Claro, SP, 13506-900, Brazil
- New York University Abu Dhabi, Saadiyat Island, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Maurício Bacci
- Centro de Estudos de Insetos Sociais, Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista - Campus Rio Claro, Rio Claro, SP, 13506-900, Brazil
| | - Paulo S Oliveira
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil.
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13
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Nepel M, Pfeifer J, Oberhauser FB, Richter A, Woebken D, Mayer VE. Nitrogen fixation by diverse diazotrophic communities can support population growth of arboreal ants. BMC Biol 2022; 20:135. [PMID: 35681192 PMCID: PMC9185989 DOI: 10.1186/s12915-022-01289-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/31/2022] [Indexed: 11/17/2022] Open
Abstract
Background Symbiotic ant-plant associations, in which ants live on plants, feed on plant-provided food, and protect host trees against threats, are ubiquitous across the tropics, with the Azteca-Cecropia associations being amongst the most widespread interactions in the Neotropics. Upon colonization of Cecropia’s hollow internodes, Azteca queens form small patches with plant parenchyma, which are then used as waste piles when the colony grows. Patches—found in many ant-plant mutualisms—are present throughout the colony life cycle and may supplement larval food. Despite their initial nitrogen (N)-poor substrate, patches in Cecropia accommodate fungi, nematodes, and bacteria. In this study, we investigated the atmospheric N2 fixation as an N source in patches of early and established ant colonies. Results Via 15N2 tracer assays, N2 fixation was frequently detected in all investigated patch types formed by three Azteca ant species. Quantified fixation rates were similar in early and established ant colonies and higher than in various tropical habitats. Based on amplicon sequencing, the identified microbial functional guild—the diazotrophs—harboring and transcribing the dinitrogenase reductase (nifH) gene was highly diverse and heterogeneous across Azteca colonies. The community composition differed between early and established ant colonies and partly between the ant species. Conclusions Our data show that N2 fixation can result in reasonable amounts of N in ant colonies, which might not only enable bacterial, fungal, and nematode growth in the patch ecosystems but according to our calculations can even support the growth of ant populations. The diverse and heterogeneous diazotrophic community implies a functional redundancy, which could provide the ant-plant-patch system with a higher resilience towards changing environmental conditions. Hence, we propose that N2 fixation represents a previously unknown potential to overcome N limitations in arboreal ant colonies. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01289-0.
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Affiliation(s)
- Maximilian Nepel
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria. .,Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Josephine Pfeifer
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Felix B Oberhauser
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Veronika E Mayer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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14
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Béchade B, Hu Y, Sanders JG, Cabuslay CS, Łukasik P, Williams BR, Fiers VJ, Lu R, Wertz JT, Russell JA. Turtle ants harbor metabolically versatile microbiomes with conserved functions across development and phylogeny. FEMS Microbiol Ecol 2022; 98:6602351. [PMID: 35660864 DOI: 10.1093/femsec/fiac068] [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: 01/07/2022] [Revised: 05/16/2022] [Accepted: 06/01/2022] [Indexed: 11/14/2022] Open
Abstract
Gut bacterial symbionts can support animal nutrition by facilitating digestion and providing valuable metabolites. However, changes in symbiotic roles between immature and adult stages are not well documented, especially in ants. Here, we explored the metabolic capabilities of microbiomes sampled from herbivorous turtle ant (Cephalotes sp.) larvae and adult workers through (meta)genomic screening and in vitro metabolic assays. We reveal that larval guts harbor bacterial symbionts with impressive metabolic capabilities, including catabolism of plant and fungal recalcitrant dietary fibers and energy-generating fermentation. Additionally, several members of the specialized adult gut microbiome, sampled downstream of an anatomical barrier that dams large food particles, show a conserved potential to depolymerize many dietary fibers. Symbionts from both life stages have the genomic capacity to recycle nitrogen and synthesize amino acids and B-vitamins. With help of their gut symbionts, including several bacteria likely acquired from the environment, turtle ant larvae may aid colony digestion and contribute to colony-wide nitrogen, B-vitamin and energy budgets. In addition, the conserved nature of the digestive capacities among adult-associated symbionts suggests that nutritional ecology of turtle ant colonies has long been shaped by specialized, behaviorally-transferred gut bacteria with over 45 million years of residency.
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Affiliation(s)
- Benoît Béchade
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Yi Hu
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America.,State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jon G Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Christian S Cabuslay
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Piotr Łukasik
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Bethany R Williams
- Department of Biology, Calvin College, Grand Rapids, Michigan, United States of America
| | - Valerie J Fiers
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Richard Lu
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - John T Wertz
- Department of Biology, Calvin College, Grand Rapids, Michigan, United States of America
| | - Jacob A Russell
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
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15
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Zhou Z, Huang H, Che X. Bacterial Communities in the Feces of Laboratory Reared Gampsocleis gratiosa (Orthoptera: Tettigoniidae) across Different Developmental Stages and Sexes. INSECTS 2022; 13:insects13040361. [PMID: 35447806 PMCID: PMC9024567 DOI: 10.3390/insects13040361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 12/10/2022]
Abstract
Simple Summary Many insects host a diverse gut microbial community, ranging from pathogenic to obligate mutualistic organisms. Little is known about the bacteria associated with katydids. Gampsocleis gratiosa (Orthoptera, Tettigoniidae) is an economically important singing pet in China. In the present study, the bacterial communities of the laboratory-reared G. gratiosa feces were characterized using Illumina sequencing of the 16S rDNA V3-V4 region. Abstract We used Illumina sequencing of the 16S rDNA V3-V4 region to identify the bacterial community in laboratory-reared G. gratiosa feces across different developmental stages (1st–7th instar nymph day 0, and 0-, 7-, 14-, and 21-day adult) and sexes. In total, 14,480,559 high-quality reads were clustered into 2982 species-level operational taxonomic units (OTUs), with an average of 481.197 (±137.366) OTUs per sample. These OTUs were assigned into 25 phyla, 42 classes, 60 orders, 116 families, 241 genera, and some unclassified groups. Only 21 core OTUs were shared by all samples. The most representative phylum was Proteobacteria, followed by Firmicutes, Bacteroidetes, and Acidobacteria. At the genus level, Kluyvera (387 OTUs), Obesumbacterium (339 OTUs), Buttiauxella (296 OTUs), Lactobacillus (286 OTUs), and Hafnia (152 OTUs) were dominant bacteria. The early-instar nymphs harbored a similar bacterial community with other developmental stages, which contain higher species diversity. Both principal coordinate analysis (PCoA) and non-metric multidimensional scaling analysis (NMDS) failed to provide a clear clustering based on the developmental stages and sexes. Overall, we assume that G. gratiosa transmits bacteria vertically by eating contaminated eggshells, and both developmental stages and sexes had no significant effect on the fecal bacterial community.
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Affiliation(s)
- Zhijun Zhou
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China; (H.H.); (X.C.)
- Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
- Correspondence:
| | - Huimin Huang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China; (H.H.); (X.C.)
| | - Xuting Che
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China; (H.H.); (X.C.)
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16
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Zheng Z, Zhao M, Zhang Z, Hu X, Xu Y, Wei C, He H. Lactic Acid Bacteria Are Prevalent in the Infrabuccal Pockets and Crops of Ants That Prefer Aphid Honeydew. Front Microbiol 2022; 12:785016. [PMID: 35126329 PMCID: PMC8814368 DOI: 10.3389/fmicb.2021.785016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/09/2021] [Indexed: 01/04/2023] Open
Abstract
Ants are evolutionarily successful species and occupy diverse trophic and habitat niches on the earth. To fulfill dietary requirements, ants have established commensalism with both sap-feeding insects and bacteria. In this study, we used high-throughput sequencing of the bacterial 16S rRNA gene to characterize the bacterial composition and structure of the digestive tracts in three species of Formica ants and Lasius niger (Linnaeus)—species that predominantly feed on honeydew secreted by aphids. We found that bacterial communities displayed species- and colony-level signatures, and that bacterial communities in the infrabuccal pockets and crops were different from those in the midguts and hindguts. Lactobacillus and Wolbachia were dominant in the infrabuccal pockets and crops of workers, whereas Wolbachia was dominant in the midguts, hindguts and brood (larvae, pupae and cocoons). To learn more about the dominant Lactobacillus in ants, we assessed its prevalence in a wide range of aphid-tending ants using diagnostic PCR. We found that Lactobacillus was more prevalent in Formicinae than in Myrmicinae species. We also isolated four strains of lactic acid bacteria (Lactobacillus sanfranciscensis, Lactobacillus lindneri, Weissella cibaria and Fructobacillus sp.) from the infrabuccal pockets and crops of aphid-tending ants using a culture-dependent method. Two predominant lactic acid bacterial isolates, Lactobacillus sanfranciscensis (La2) and Weissella cibaria (La3), exhibited abilities in catabolizing sugars (sucrose, trehalose, melezitose and raffinose) known to be constituents of hemipteran honeydew. These findings contribute to further understanding the association between ants, aphids and bacteria, and provide additional information on the function of lactic acid bacteria in ants.
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Affiliation(s)
- Zhou Zheng
- Key Laboratory of National Forestry and Grassland Administration for Control of Forest Biological Disasters in Western China, College of Forestry, Northwest A&F University, Yangling, China
| | - Mengqin Zhao
- Key Laboratory of National Forestry and Grassland Administration for Control of Forest Biological Disasters in Western China, College of Forestry, Northwest A&F University, Yangling, China
| | - Zhijun Zhang
- Key Laboratory of National Forestry and Grassland Administration for Control of Forest Biological Disasters in Western China, College of Forestry, Northwest A&F University, Yangling, China
| | - Xin Hu
- Key Laboratory of National Forestry and Grassland Administration for Control of Forest Biological Disasters in Western China, College of Forestry, Northwest A&F University, Yangling, China
| | - Yang Xu
- Key Laboratory of National Forestry and Grassland Administration for Control of Forest Biological Disasters in Western China, College of Forestry, Northwest A&F University, Yangling, China
| | - Cong Wei
- Key Laboratory of Plant Protection Resources and Pest Management, College of Plant Protection, Northwest A&F University, Yangling, China
- *Correspondence: Cong Wei,
| | - Hong He
- Key Laboratory of National Forestry and Grassland Administration for Control of Forest Biological Disasters in Western China, College of Forestry, Northwest A&F University, Yangling, China
- Hong He,
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17
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Zhang W, Liu F, Zhu Y, Han R, Xu L, Liu J. Differing Dietary Nutrients and Diet-Associated Bacteria Has Limited Impact on Spider Gut Microbiota Composition. Microorganisms 2021; 9:2358. [PMID: 34835483 PMCID: PMC8618231 DOI: 10.3390/microorganisms9112358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/18/2022] Open
Abstract
Spiders are a key predator of insects across ecosystems and possess great potential as pest control agents. Unfortunately, it is difficult to artificially cultivate multiple generations of most spider species. Since gut bacterial flora has been shown to significantly alter nutrient availability, it is plausible that the spiders' microbial community plays a key role in their unsuccessful breeding. However, both the gut microbial composition and its influencing factors in many spiders remain a mystery. In this study, the gut microbiota of Campanicola campanulata, specialists who prey on ants and are widely distributed across China, was characterized. After, the impact of diet and diet-associated bacteria on gut bacterial composition was evaluated. First, two species of prey ants (Lasius niger and Tetramorium caespitum) were collected from different locations and fed to C. campanulata. For each diet, we then profiled the nutritional content of the ants, as well as the bacterial communities of both the ants and spiders. Results showed that the protein and carbohydrate content varied between the two prey ant species. We isolated 682 genera from 356 families in the ants (dominant genera including Pseudomonas, Acinetobacter, Paraburkholderia, Staphylococcus, and Novosphingobium), and 456 genera from 258 families in the spiders (dominated by Pseudomonas). However, no significant differences were found in the gut microbiota of spiders that were fed the differing ants. Together, these results indicate that nutritional variation and diet-associated bacterial differences have a limited impact on the microbial composition of spider guts, highlighting that spiders may have a potentially stable internal environment and lay the foundation for future investigations into gut microbiota.
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Affiliation(s)
- Wang Zhang
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Science, Hubei University, Wuhan 430062, China;
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, College of Life Sciences, Hubei University, Wuhan 430062, China; (F.L.); (Y.Z.)
| | - Fengjie Liu
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, College of Life Sciences, Hubei University, Wuhan 430062, China; (F.L.); (Y.Z.)
| | - Yang Zhu
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, College of Life Sciences, Hubei University, Wuhan 430062, China; (F.L.); (Y.Z.)
| | - Runhua Han
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA;
| | - Letian Xu
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, College of Life Sciences, Hubei University, Wuhan 430062, China; (F.L.); (Y.Z.)
| | - Jie Liu
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Science, Hubei University, Wuhan 430062, China;
- The State Key Laboratory of Biocatalysis and Enzyme Engineering of China, College of Life Sciences, Hubei University, Wuhan 430062, China; (F.L.); (Y.Z.)
- School of Nuclear Technology and Chemistry, Biology University of Science and Technology, Xianning 437100, China
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18
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Drew GC, Budge GE, Frost CL, Neumann P, Siozios S, Yañez O, Hurst GDD. Transitions in symbiosis: evidence for environmental acquisition and social transmission within a clade of heritable symbionts. THE ISME JOURNAL 2021; 15:2956-2968. [PMID: 33941888 PMCID: PMC8443716 DOI: 10.1038/s41396-021-00977-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 03/17/2021] [Accepted: 04/06/2021] [Indexed: 02/03/2023]
Abstract
A dynamic continuum exists from free-living environmental microbes to strict host-associated symbionts that are vertically inherited. However, knowledge of the forces that drive transitions in symbiotic lifestyle and transmission mode is lacking. Arsenophonus is a diverse clade of bacterial symbionts, comprising reproductive parasites to coevolving obligate mutualists, in which the predominant mode of transmission is vertical. We describe a symbiosis between a member of the genus Arsenophonus and the Western honey bee. The symbiont shares common genomic and predicted metabolic properties with the male-killing symbiont Arsenophonus nasoniae, however we present multiple lines of evidence that the bee Arsenophonus deviates from a heritable model of transmission. Field sampling uncovered spatial and seasonal dynamics in symbiont prevalence, and rapid infection loss events were observed in field colonies and laboratory individuals. Fluorescent in situ hybridisation showed Arsenophonus localised in the gut, and detection was rare in screens of early honey bee life stages. We directly show horizontal transmission of Arsenophonus between bees under varying social conditions. We conclude that honey bees acquire Arsenophonus through a combination of environmental exposure and social contacts. These findings uncover a key link in the Arsenophonus clades trajectory from free-living ancestral life to obligate mutualism, and provide a foundation for studying transitions in symbiotic lifestyle.
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Affiliation(s)
- Georgia C Drew
- Department of Zoology, University of Oxford, Oxford, UK.
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
| | - Giles E Budge
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Crystal L Frost
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Stefanos Siozios
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Orlando Yañez
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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19
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Morris MT, Hauton C, Baylay AJ, Peruzza L, Targett TE, Ciotti BJ. Spatial variation in the gastrointestinal microbiome, diet, and nutritional condition of a juvenile flatfish among coastal habitats. MARINE ENVIRONMENTAL RESEARCH 2021; 170:105413. [PMID: 34284178 DOI: 10.1016/j.marenvres.2021.105413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/30/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Gut microbiota are important for the health, fitness and development of animal hosts, but little is known about these assemblages in wild populations of fish. Such knowledge is particularly important for juvenile life stages where nutritional intake critically determines early development, growth, and ultimately recruitment. We characterise the microbiome inhabiting the gut of young-of-the-year European plaice ('YOY plaice') on sandy beaches, their key juvenile habitat, and examine how these microbial communities vary spatially in relation to diet and nutritional condition of their plaice hosts. Body size, diet (stomach fullness and eukaryotic 18S ribosomal sequencing), nutritional condition (RNA:DNA) and gut microbiota (16S prokaryotic ribosomal sequencing) were compared in fish at two spatial scales: between beaches separated by 10s of kilometres and between sites at different depths on the same beach, separated by 10s of metres. The main microbial phyla in YOY plaice guts were Proteobacteria, Spirochaetes, Tenericutes and Verrucomicrobiae. Within the Proteobacteria there was an unusual dominance of Alphaproteobacteria. Differences in body size, diet and nutritional condition of YOY plaice between beaches were accompanied by differences in gut microbial assemblage structure. Notably, substantially reduced nutritional condition and size at one of the beaches was associated with lower stomach fullness, reduced consumption of annelids and differences in the abundance and presence of specific microbial taxa. Differences were also detected in microbial assemblages, body size, and diet between depths within the same nursery beach, although stomach fullness and nutritional condition did not vary significantly. The functional links between the environment, gut microbiota, and their hosts are potentially important mediators of the development of young fish through critical life stages. Our study indicates that these links need to be addressed at 10 km and even 10 m scales to capture the variability observed in wild populations of juvenile fish.
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Affiliation(s)
- Marc T Morris
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre Southampton, European Way, Southampton, SO14 3ZH, UK; Present address: Australian Centre for Ecogenomics, University of Queensland, Brisbane, St Lucia, 4072, Australia
| | - Chris Hauton
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre Southampton, European Way, Southampton, SO14 3ZH, UK
| | - Alison J Baylay
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre Southampton, European Way, Southampton, SO14 3ZH, UK
| | - Luca Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Timothy E Targett
- School of Marine Science and Policy, University of Delaware, Lewes, DE 19958, USA
| | - Benjamin J Ciotti
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK.
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20
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Lindström S, Timonen S, Sundström L. The bacterial and fungal community composition in time and space in the nest mounds of the ant Formica exsecta (Hymenoptera: Formicidae). Microbiologyopen 2021; 10:e1201. [PMID: 34459553 PMCID: PMC8289489 DOI: 10.1002/mbo3.1201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 11/09/2022] Open
Abstract
In a subarctic climate, the seasonal shifts in temperature, precipitation, and plant cover drive the temporal changes in the microbial communities in the topsoil, forcing soil microbes to adapt or decline. Many organisms, such as mound-building ants, survive the cold winter owing to the favorable microclimate in their nest mounds. We have previously shown that the microbial communities in the nest of the ant Formica exsecta are significantly different from those in the surrounding bulk soil. In the current study, we identified taxa, which were consistently present in the nests over a study period of three years. Some taxa were also significantly enriched in the nest samples compared with spatially corresponding reference soils. We show that the bacterial communities in ant nests are temporally stable across years, whereas the fungal communities show greater variation. It seems that the activities of the ants contribute to unique biochemical processes in the secluded nest environment, and create opportunities for symbiotic interactions between the ants and the microbes. Over time, the microbial communities may come to diverge, due to drift and selection, especially given the long lifespan (up to 30 years) of the ant colonies.
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Affiliation(s)
- Stafva Lindström
- Organismal and Evolutionary Biology Research ProgrammeFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Tvärminne Zoological StationHankoFinland
- Department of MicrobiologyUniversity of HelsinkiHelsinkiFinland
| | - Sari Timonen
- Department of MicrobiologyUniversity of HelsinkiHelsinkiFinland
| | - Liselotte Sundström
- Organismal and Evolutionary Biology Research ProgrammeFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Tvärminne Zoological StationHankoFinland
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21
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Flynn PJ, D'Amelio CL, Sanders JG, Russell JA, Moreau CS. Localization of bacterial communities within gut compartments across Cephalotes turtle ants. Appl Environ Microbiol 2021; 87:AEM.02803-20. [PMID: 33579688 PMCID: PMC8091110 DOI: 10.1128/aem.02803-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/05/2021] [Indexed: 02/07/2023] Open
Abstract
Microbial communities within the animal digestive tract often provide important functions for their hosts. The composition of eukaryotes' gut bacteria can be shaped by host diet, vertical bacterial transmission, and physiological variation within the digestive tract. In several ant taxa, recent findings have demonstrated that nitrogen provisioning by symbiotic bacteria makes up for deficiencies in herbivorous diets. Using 16S rRNA amplicon sequencing and qPCR, this study examined bacterial communities at a fine scale across one such animal group, the turtle ant genus Cephalotes We analyzed the composition and colonization density across four portions of the digestive tract to understand how bacterial diversity is structured across gut compartments, potentially allowing for specific metabolic functions of benefit to the host. In addition, we aimed to understand if caste differentiation or host relatedness influences the gut bacterial communities of Cephalotes ants. Microbial communities were found to vary strongly across Cephalotes gut compartments in ways that transcend both caste and host phylogeny. Despite this, caste and host phylogeny still have detectable effects. We demonstrated microbial community divergence across gut compartments, possibly due to the varying function of each gut compartment for digestion.IMPORTANCE Gut compartments play an important role in structuring the microbial community within individual ants. The gut chambers of the turtle ant digestive tract differ remarkably in symbiont abundance and diversity. Furthermore, caste type explains some variation in the microbiome composition. Finally, the evolutionary history of the Cephalotes species structures the microbiome in our study, which elucidates a trend in which related ants maintain related microbiomes, conceivably owing to co-speciation. Amazingly, gut compartment-specific signatures of microbial diversity, relative abundance, composition, and abundance have been conserved over Cephalotes evolutionary history, signifying that this symbiosis has been largely stable for over 50 million years.
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Affiliation(s)
- Peter J Flynn
- University of Chicago, Committee on Evolutionary Biology, Chicago, IL, 60605 USA
| | - Catherine L D'Amelio
- Drexel University, Department of Biodiversity, Earth and Environmental Science, Philadelphia, PA, 19104 USA
| | - Jon G Sanders
- Cornell University, Department Ecology and Evolutionary Biology, Ithaca, NY, 14850 USA
| | - Jacob A Russell
- Drexel University, Department of Biodiversity, Earth and Environmental Science, Philadelphia, PA, 19104 USA
| | - Corrie S Moreau
- Cornell University, Department Ecology and Evolutionary Biology, Ithaca, NY, 14850 USA
- Cornell University, Department of Entomology, Ithaca, NY, 14850 USA
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22
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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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23
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Bacterial Composition and Diversity of the Digestive Tract of Odontomachus monticola Emery and Ectomomyrmex javanus Mayr. INSECTS 2021; 12:insects12020176. [PMID: 33671250 PMCID: PMC7922086 DOI: 10.3390/insects12020176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/31/2021] [Accepted: 02/05/2021] [Indexed: 01/04/2023]
Abstract
Simple Summary Bacteria are considered to be one of the compelling participants in ant dietary differentiation. The digestive tract of ants is characterized by a developed crop, an elaborate proventriculus, and an infrabuccal pocket, which is a special filtrating structure in the mouthparts, adapting to their special trophallaxis behavior. Ponerine ants are true predators and a primitive ant group; notably, their gut bacterial communities get less attention than herbivorous ants. In this study, we investigated the composition and diversity of bacterial communities in the digestive tract and the infrabuccal pockets of two widely distributed ponerine species (Odontomachus monticola Emery and Ectomomyrmex javanus Mayr) in northwestern China using high-throughput sequencing of the bacterial 16S rRNA gene. The results revealed that, not only do the gut bacterial communities display significant interspecies differences, but they also possess apparent intercolony characteristics. Within each colony, the bacterial communities were highly similar between each gut section (crops, midguts, and hindguts) of workers, but significantly different from their infrabuccal pockets, which were similar to bacterial communities in larvae of O. monticola. The relationship of the bacterial communities among the infrabuccal pockets, gut sections and larvae provide meaningful information to understand the social life and feeding behavior of ants. Abstract Ponerine ants are generalist predators feeding on a variety of small arthropods, annelids, and isopods; however, knowledge of their bacterial communities is rather limited. This study investigated the bacterial composition and diversity in the digestive tract (different gut sections and the infrabuccal pockets (IBPs)) of two ponerine ant species (Odontomachus monticola Emery and Ectomomyrmex javanus Mayr) distributed in northwestern China using high-throughput sequencing. We found that several dominant bacteria that exist in other predatory ants were also detected in these two ponerine ant species, including Wolbachia, Mesoplasma, and Spiroplasma. Bacterial communities of these two ant species were differed significantly from each other, and significant differences were also observed across their colonies, showing distinctive inter-colony characteristics. Moreover, bacterial communities between the gut sections (crops, midguts, and hindguts) of workers were highly similar within colony, but they were clearly different from those in IBPs. Further, bacterial communities in the larvae of O. monticola were similar to those in the IBPs of workers, but significantly different from those in gut sections. We presume that the bacterial composition and diversity in ponerine ants are related to their social behavior and feeding habits, and bacterial communities in the IBPs may play a potential role in their social life.
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24
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Disentangling the Relative Roles of Vertical Transmission, Subsequent Colonizations, and Diet on Cockroach Microbiome Assembly. mSphere 2021; 6:6/1/e01023-20. [PMID: 33408228 PMCID: PMC7845597 DOI: 10.1128/msphere.01023-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A multitude of factors affect the assemblies of complex microbial communities associated with animal hosts, with implications for community flexibility, resilience, and long-term stability; however, their relative effects have rarely been deduced. Here, we use a tractable lab model to quantify the relative and combined effects of parental transmission (egg case microbiome present/reduced), gut inocula (cockroach versus termite gut provisioned), and varying diets (matched or unmatched with gut inoculum source) on gut microbiota structure of hatchlings of the omnivorous cockroach Shelfordella lateralis using 16S rRNA gene (rDNA) amplicon sequencing. We show that the presence of a preexisting bacterial community via vertical transmission of microbes on egg cases reduces subsequent microbial invasion, suggesting priority effects that allow initial colonizers to take a strong hold and which stabilize the microbiome. However, subsequent inoculation sources more strongly affect ultimate community composition and their ecological networks, with distinct host-taxon-of-origin effects on which bacteria establish. While this is so, communities respond flexibly to specific diets in ways that consequently impact predicted community functions. In conclusion, our findings suggest that inoculations drive communities toward different stable states depending on colonization and extinction events, through ecological host-microbe relations and interactions with other gut bacteria, while diet in parallel shapes the functional capabilities of these microbiomes. These effects may lead to consistent microbial communities that maximize the extended phenotype that the microbiota provides the host, particularly if microbes spend most of their lives in host-associated environments.IMPORTANCE When host fitness is dependent on gut microbiota, microbial community flexibility and reproducibility enhance host fitness by allowing fine-tuned environmental tracking and sufficient stability for host traits to evolve. Our findings lend support to the importance of vertically transmitted early-life microbiota as stabilizers, through interactions with potential colonizers, which may contribute to ensuring that the microbiota aligns within host fitness-enhancing parameters. Subsequent colonizations are driven by microbial composition of the sources available, and we confirm that host-taxon-of-origin affects stable subsequent communities, while communities at the same time retain sufficient flexibility to shift in response to available diets. Microbiome structure is thus the result of the relative impact and combined effects of inocula and fluctuations driven by environment-specific microbial sources and digestive needs. These affect short-term community structure on an ecological time scale but could ultimately shape host species specificities in microbiomes across evolutionary time, if environmental conditions prevail.
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25
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Tragust S, Herrmann C, Häfner J, Braasch R, Tilgen C, Hoock M, Milidakis MA, Gross R, Feldhaar H. Formicine ants swallow their highly acidic poison for gut microbial selection and control. eLife 2020; 9:e60287. [PMID: 33138912 PMCID: PMC7609056 DOI: 10.7554/elife.60287] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/14/2020] [Indexed: 12/23/2022] Open
Abstract
Animals continuously encounter microorganisms that are essential for health or cause disease. They are thus challenged to control harmful microbes while allowing the acquisition of beneficial microbes. This challenge is likely especially important for social insects with respect to microbes in food, as they often store food and exchange food among colony members. Here we show that formicine ants actively swallow their antimicrobial, highly acidic poison gland secretion. The ensuing acidic environment in the stomach, the crop, can limit the establishment of pathogenic and opportunistic microbes ingested with food and improve the survival of ants when faced with pathogen contaminated food. At the same time, crop acidity selectively allows acquisition and colonization by Acetobacteraceae, known bacterial gut associates of formicine ants. This suggests that swallowing of the poison in formicine ants acts as a microbial filter and that antimicrobials have a potentially widespread but so far underappreciated dual role in host-microbe interactions.
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Affiliation(s)
- Simon Tragust
- Animal Ecology I, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, UniversitätsstraßeBayreuthGermany
| | - Claudia Herrmann
- Animal Ecology I, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, UniversitätsstraßeBayreuthGermany
| | - Jane Häfner
- Animal Ecology I, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, UniversitätsstraßeBayreuthGermany
| | - Ronja Braasch
- Animal Ecology I, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, UniversitätsstraßeBayreuthGermany
| | - Christina Tilgen
- Animal Ecology I, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, UniversitätsstraßeBayreuthGermany
| | - Maria Hoock
- Animal Ecology I, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, UniversitätsstraßeBayreuthGermany
| | - Margarita Artemis Milidakis
- Animal Ecology I, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, UniversitätsstraßeBayreuthGermany
| | - Roy Gross
- Microbiology, Biocenter, University of Würzburg, Am HublandWürzburgGermany
| | - Heike Feldhaar
- Animal Ecology I, Bayreuth Center for Ecology and Environmental Research (BayCEER), University of Bayreuth, UniversitätsstraßeBayreuthGermany
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26
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Kucuk RA. Gut Bacteria in the Holometabola: A Review of Obligate and Facultative Symbionts. JOURNAL OF INSECT SCIENCE (ONLINE) 2020; 20:5893943. [PMID: 32809024 PMCID: PMC7433766 DOI: 10.1093/jisesa/ieaa084] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Indexed: 06/11/2023]
Abstract
The diversity and ecological variety of Holometabola foregrounds a wide array of dynamic symbiotic relationships with gut-dwelling bacteria. A review of the literature highlights that holometabolous insects rely on both obligate bacteria and facultative bacteria living in their guts to satisfy a number of physiological needs. The driving forces behind these differing relationships can be hypothesized through the scrutiny of bacterial associations with host gut morphology, and transmission of bacteria within a given host taxon. Our knowledge of the evolution of facultative or obligate symbiotic bacteria in holometabolan systems is further enhanced by an assessment of the various services the bacteria provide, including nutrition, immune system health, and development. The diversity of Holometabola can thus be examined through an assessment of known bacterial partnerships within the orders of Holometabola.
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Affiliation(s)
- R A Kucuk
- Clemson University, Poole Agricultural Center, Clemson, SC
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27
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Colborn AS, Kuntze CC, Gadsden GI, Harris NC. Spatial variation in diet-microbe associations across populations of a generalist North American carnivore. J Anim Ecol 2020; 89:1952-1960. [PMID: 32445202 DOI: 10.1111/1365-2656.13266] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 05/05/2020] [Indexed: 11/28/2022]
Abstract
Generalist species, by definition, exhibit variation in niche attributes that promote survival in changing environments. Increasingly, phenotypes previously associated with a species, particularly those with wide or expanding ranges, are dissolving and compelling greater emphasis on population-level characteristics. In the present study, we assessed spatial variation in diet characteristics, gut microbiome and associations between these two ecological traits across populations of coyotes Canis latrans. We highlight the influence of the carnivore community in shaping these relationships, as the coyote varied from being an apex predator to a subordinate, mesopredator across sampled populations. We implemented a scat survey across three distinct coyote populations in Michigan, USA. We used carbon (δ13 C) and nitrogen (δ15 N) isotopic values to reflect consumption patterns and trophic level, respectively. Corresponding samples were also paired with 16S rRNA sequencing to describe the microbial community and correlate with isotopic values. Although consumption patterns were comparable, we found spatial variation in trophic level among coyote populations. Specifically, δ15 N was highest where coyotes were the apex predator and lowest where coyotes co-occurred with grey wolves Canis lupus. The gut microbial community exhibited marked spatial variation across populations with the lowest operational taxonomic units diversity found where coyotes occurred at their lowest trophic level. Bacteriodes and Fusobacterium dominated the microbiome and were positively correlated across all populations. We found no correlation between δ13 C and microbial community attributes. However, positive associations between δ15 N and specific microbial genera increased as coyotes ascended trophic levels. Coyotes provide a model for exploring implications of niche plasticity because they are a highly adaptable, wide-ranging omnivore. As coyotes continue to vary in trophic position and expand their geographic range, we might expect increased divergence within their microbial community, changes in physiology and alterations in behaviour.
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Affiliation(s)
- A Shawn Colborn
- Applied Wildlife Ecology Lab, Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Corbin C Kuntze
- Applied Wildlife Ecology Lab, Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel I Gadsden
- Applied Wildlife Ecology Lab, Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Nyeema C Harris
- Applied Wildlife Ecology Lab, Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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28
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Bar-Shmuel N, Behar A, Segoli M. What do we know about biological nitrogen fixation in insects? Evidence and implications for the insect and the ecosystem. INSECT SCIENCE 2020; 27:392-403. [PMID: 31207108 DOI: 10.1111/1744-7917.12697] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/22/2019] [Accepted: 06/11/2019] [Indexed: 06/09/2023]
Abstract
Many insects feed on a low-nitrogen diet, and the origin of their nitrogen supply is poorly understood. It has been hypothesized that some insects rely on nitrogen-fixing bacteria (diazotrophs) to supplement their diets. Nitrogen fixation by diazotrophs has been extensively studied and convincingly demonstrated in termites, while evidence for the occurrence and role of nitrogen fixation in the diet of other insects is less conclusive. Here, we summarize the methods to detect nitrogen fixation in insects and review the available evidence for its occurrence (focusing on insects other than termites). We distinguish between three aspects of nitrogen fixation investigations: (i) detecting the presence of potential diazotrophs; (ii) detecting the activity of the nitrogen-fixing enzyme; and (iii) detecting the assimilation of fixed nitrogen into the insect tissues. We show that although evidence from investigations of the first aspect reveals ample opportunities for interactions with potential diazotrophs in a variety of insects, demonstrations of actual biological nitrogen fixation and the assimilation of fixed nitrogen are restricted to very few insect groups, including wood-feeding beetles, fruit flies, leafcutter ants, and a wood wasp. We then discuss potential implications for the insect's fitness and for the ecosystem as a whole. We suggest that combining these multiple approaches is crucial for the study of nitrogen fixation in insects, and argue that further demonstrations are desperately needed in order to determine the relative importance of diazotrophs for insect diet and fitness, as well as to evaluate their overall impact on the ecosystem.
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Affiliation(s)
- Nitsan Bar-Shmuel
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Adi Behar
- Kimron Veterinary Institute, Department of Parasitology, Bet Dagan, Israel
| | - Michal Segoli
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
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29
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Interactions between social groups of colobus monkeys (Colobus vellerosus) explain similarities in their gut microbiomes. Anim Behav 2020. [DOI: 10.1016/j.anbehav.2020.02.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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30
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Development but not diet alters microbial communities in the Neotropical arboreal trap jaw ant Daceton armigerum: an exploratory study. Sci Rep 2020; 10:7350. [PMID: 32355187 PMCID: PMC7192945 DOI: 10.1038/s41598-020-64393-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/31/2020] [Indexed: 01/01/2023] Open
Abstract
To better understand the evolutionary significance of symbiotic interactions in nature, microbiome studies can help to identify the ecological factors that may shape host-associated microbial communities. In this study we explored both 16S and 18S rRNA microbial communities of D. armigerum from both wild caught individuals collected in the Amazon and individuals kept in the laboratory and fed on controlled diets. We also investigated the role of colony, sample type, development and caste on structuring microbial communities. Our bacterial results (16S rRNA) reveal that (1) there are colony level differences between bacterial communities; (2) castes do not structure communities; (3) immature stages (brood) have different bacterial communities than adults; and 4) individuals kept in the laboratory with a restricted diet showed no differences in their bacterial communities from their wild caught nest mates, which could indicate the presence of a stable and persistent resident bacterial community in this host species. The same categories were also tested for microbial eukaryote communities (18S rRNA), and (5) developmental stage has an influence on the diversity recovered; (6) the diversity of taxa recovered has shown this can be an important tool to understand additional aspects of host biology and species interactions.
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31
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Kennedy SR, Tsau S, Gillespie R, Krehenwinkel H. Are you what you eat? A highly transient and prey-influenced gut microbiome in the grey house spider Badumna longinqua. Mol Ecol 2020; 29:1001-1015. [PMID: 32011756 DOI: 10.1111/mec.15370] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/16/2020] [Accepted: 01/29/2020] [Indexed: 01/01/2023]
Abstract
Stable core microbial communities have been described in numerous animal species and are commonly associated with fitness benefits for their hosts. Recent research, however, highlights examples of species whose microbiota are transient and environmentally derived. Here, we test the effect of diet on gut microbial community assembly in the spider Badumna longinqua. Using 16S rRNA gene amplicon sequencing combined with quantitative PCR, we analyzed diversity and abundance of the spider's gut microbes, and simultaneously characterized its prey communities using nuclear rRNA markers. We found a clear correlation between community similarity of the spider's insect prey and gut microbial DNA, suggesting that microbiome assembly is primarily diet-driven. This assumption is supported by a feeding experiment, in which two types of prey-crickets and fruit flies-both substantially altered microbial diversity and community similarity between spiders, but did so in different ways. After cricket consumption, numerous cricket-derived microbes appeared in the spider's gut, resulting in a rapid homogenization of microbial communities among spiders. In contrast, few prey-associated bacteria were detected after consumption of fruit flies; instead, the microbial community was remodelled by environmentally sourced microbes, or abundance shifts of rare taxa in the spider's gut. The reshaping of the microbiota by both prey taxa mimicked a stable core microbiome in the spiders for several weeks post feeding. Our results suggest that the spider's gut microbiome undergoes pronounced temporal fluctuations, that its assembly is dictated by the consumed prey, and that different prey taxa may remodel the microbiota in drastically different ways.
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Affiliation(s)
- Susan R Kennedy
- Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA.,Universität Trier Biogeographie, Trier, Germany.,Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Sophia Tsau
- Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
| | - Rosemary Gillespie
- Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
| | - Henrik Krehenwinkel
- Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA.,Universität Trier Biogeographie, Trier, Germany
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32
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Kaczmarczyk-Ziemba A, Zagaja M, Wagner GK, Pietrykowska-Tudruj E, Staniec B. First Insight into Microbiome Profiles of Myrmecophilous Beetles and Their Host, Red Wood Ant Formica polyctena (Hymenoptera: Formicidae)-A Case Study. INSECTS 2020; 11:E134. [PMID: 32092972 PMCID: PMC7073670 DOI: 10.3390/insects11020134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/10/2020] [Accepted: 02/17/2020] [Indexed: 01/23/2023]
Abstract
Formica polyctena belongs to the red wood ant species group. Its nests provide a stable, food rich, and temperature and humidity controlled environment, utilized by a wide range of species, called myrmecophiles. Here, we used the high-throughput sequencing of the 16S rRNA gene on the Illumina platform for identification of the microbiome profiles of six selected myrmecophilous beetles (Dendrophilus pygmaeus, Leptacinus formicetorum, Monotoma angusticollis, Myrmechixenus subterraneus, Ptenidium formicetorum and Thiasophila angulata) and their host F. polyctena. Analyzed bacterial communities consisted of a total of 23 phyla, among which Proteobacteria, Actinobacteria, and Firmicutes were the most abundant. Two known endosymbionts-Wolbachia and Rickettsia-were found in the analyzed microbiome profiles and Wolbachia was dominant in bacterial communities associated with F. polyctena, M. subterraneus, L. formicetorum and P. formicetorum (>90% of reads). In turn, M. angusticollis was co-infected with both Wolbachia and Rickettsia, while in the microbiome of T. angulata, the dominance of Rickettsia has been observed. The relationships among the microbiome profiles were complex, and no relative abundance pattern common to all myrmecophilous beetles tested was observed. However, some subtle, species-specific patterns have been observed for bacterial communities associated with D. pygmaeus, M. angusticollis, and T. angulata.
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Affiliation(s)
- Agnieszka Kaczmarczyk-Ziemba
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Mirosław Zagaja
- Isobolographic Analysis Laboratory, Institute of Rural Health, Jaczewskiego 2, 20-090 Lublin, Poland;
| | - Grzegorz K. Wagner
- Department of Zoology and Nature Protection, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland; (G.K.W.); (E.P.-T.); (B.S.)
| | - Ewa Pietrykowska-Tudruj
- Department of Zoology and Nature Protection, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland; (G.K.W.); (E.P.-T.); (B.S.)
| | - Bernard Staniec
- Department of Zoology and Nature Protection, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland; (G.K.W.); (E.P.-T.); (B.S.)
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Martins C, Moreau CS. Influence of host phylogeny, geographical location and seed harvesting diet on the bacterial community of globally distributed Pheidole ants. PeerJ 2020; 8:e8492. [PMID: 32117618 PMCID: PMC7006521 DOI: 10.7717/peerj.8492] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 12/30/2019] [Indexed: 11/20/2022] Open
Abstract
The presence of symbiotic relationships between organisms is a common phenomenon found across the tree of life. In particular, the association of bacterial symbionts with ants is an active area of study. This close relationship between ants and microbes can significantly impact host biology and is also considered one of the driving forces in ant evolution and diversification. Diet flexibility of ants may explain the evolutionary success of the group, which may be achieved by the presence of endosymbionts that aid in nutrition acquisition from a variety of food sources. With more than 1,140 species, ants from the genus Pheidole have a worldwide distribution and an important role in harvesting seeds; this behavior is believed to be a possible key innovation leading to the diversification of this group. This is the first study to investigate the bacterial community associated with Pheidole using next generation sequencing (NGS) to explore the influences of host phylogeny, geographic location and food preference in shaping the microbial community. In addition, we explore if there are any microbiota signatures related to granivory. We identified Proteobacteria and Firmicutes as the major phyla associated with these ants. The core microbiome in Pheidole (those found in >50% of all samples) was composed of 14 ASVs and the most prevalent are family Burkholderiaceae and the genera Acinetobacter, Streptococcus, Staphylococcus, Cloacibacterium and Ralstonia. We found that geographical location and food resource may influence the bacterial community of Pheidole ants. These results demonstrate that Pheidole has a relatively stable microbiota across species, which suggests the bacterial community may serve a generalized function in this group.
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Affiliation(s)
- Cíntia Martins
- Department of Biological Science, Campus Ministro Reis Velloso, Universidade Federal do Piauí, Parnaíba, Piauí, Brazil.,Department of Science and Education, Field Museum of Natural History, Chicago, IL, United States of America
| | - Corrie S Moreau
- Department of Science and Education, Field Museum of Natural History, Chicago, IL, United States of America.,Departments of Entomology and Ecology & Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
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Kaczmarczyk-Ziemba A, Zagaja M, Wagner GK, Pietrykowska-Tudruj E, Staniec B. The microbiota of the Lasius fuliginosus – Pella laticollis myrmecophilous interaction. THE EUROPEAN ZOOLOGICAL JOURNAL 2020. [DOI: 10.1080/24750263.2020.1844322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- A. Kaczmarczyk-Ziemba
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - M. Zagaja
- Isobolographic Analysis Laboratory, Institute of Rural Health, Lublin, Poland
| | - G. K. Wagner
- Department of Zoology and Nature Protection, Maria Curie-Sklodowska University, Lublin, Poland
| | - E. Pietrykowska-Tudruj
- Department of Zoology and Nature Protection, Maria Curie-Sklodowska University, Lublin, Poland
| | - B. Staniec
- Department of Zoology and Nature Protection, Maria Curie-Sklodowska University, Lublin, Poland
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Segers FHID, Kaltenpoth M, Foitzik S. Abdominal microbial communities in ants depend on colony membership rather than caste and are linked to colony productivity. Ecol Evol 2019; 9:13450-13467. [PMID: 31871657 PMCID: PMC6912891 DOI: 10.1002/ece3.5801] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/30/2019] [Accepted: 10/03/2019] [Indexed: 12/13/2022] Open
Abstract
Gut bacteria aid their host in digestion and pathogen defense, and bacterial communities that differ in diversity or composition may vary in their ability to do so. Typically, the gut microbiomes of animals living in social groups converge as members share a nest environment and frequently interact. Social insect colonies, however, consist of individuals that differ in age, physiology, and behavior, traits that could affect gut communities or that expose the host to different bacteria, potentially leading to variation in the gut microbiome within colonies. Here we asked whether bacterial communities in the abdomen of Temnothorax nylanderi ants, composed largely of the gut microbiome, differ between different reproductive and behavioral castes. We compared microbiomes of queens, newly eclosed workers, brood carers, and foragers by high-throughput 16S rRNA sequencing. Additionally, we sampled individuals from the same colonies twice, in the field and after 2 months of laboratory housing. To disentangle the effects of laboratory environment and season on microbial communities, additional colonies were collected at the same location after 2 months. There were no large differences between ant castes, although queens harbored more diverse microbial communities than workers. Instead, we found effects of colony, environment, and season on the abdominal microbiome. Interestingly, colonies with more diverse communities had produced more brood. Moreover, the queens' microbiome composition was linked to egg production. Although long-term coevolution between social insects and gut bacteria has been repeatedly evidenced, our study is the first to find associations between abdominal microbiome characteristics and colony productivity in social insects.
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Affiliation(s)
- Francisca H. I. D. Segers
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)FrankfurtGermany
- Behavioural Ecology and Social EvolutionInstitute of Organismic and Molecular EvolutionJohannes Gutenberg UniversityMainzGermany
- Present address:
Applied Bioinformatics GroupInstitute of Cell Biology & NeuroscienceGoethe UniversityFrankfurtGermany
| | - Martin Kaltenpoth
- Evolutionary EcologyInstitute of Organismic and Molecular EvolutionJohannes Gutenberg UniversityMainzGermany
| | - Susanne Foitzik
- Evolutionary EcologyInstitute of Organismic and Molecular EvolutionJohannes Gutenberg UniversityMainzGermany
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36
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Wang J, Su Q, Zhang X, Li C, Luo S, Zhou X, Zheng H. Entomomonas moraniae gen. nov., sp. nov., a member of the family Pseudomonadaceae isolated from Asian honey bee gut, possesses a highly reduced genome. Int J Syst Evol Microbiol 2019; 70:165-171. [PMID: 31560340 DOI: 10.1099/ijsem.0.003731] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The honey bee gut microbiota contains many bacterial lineages that are specific to this ecosystem. Apis cerana, raised across the Asian continent, is of great significance to the maintenance and development of ecology and agriculture in Asia. Here, we report the isolation and characterization of strain QZS01T from the gut of Apis cerana from Pingwu County, Sichuan Province, PR China. The results of phylogenetic analysis based on 16S rRNA sequences showed that strain QZS01T forms a monophyletic group together with clone sequences derived from variable insect hosts, and it shows 92% sequence similarity to its closest relative, Pseudomonas knackmussii. Strain QZS01T possesses a reduced genome (3.3 Mbp; G+C content, 38.05 mol%) compared to all other Pseudomonas species, and the whole-genome based phylogenetic reconstruction showed that strain QZS01T represents a novel genus within the family Pseudomonadaceae. Strain QZS01T is a Gram-stain-negative facultative anaerobe. It grows on brain heart infusion agar and the energy sources utilized for growth are very limited. Based on the results of genotypic and phenotypic analyses, we propose a novel genus and species, Entomomonas moraniae gen. nov., sp. nov., with the type strain QZS01T (=CGMCC 1.13498T=KCTC 62495T).
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Affiliation(s)
- Jieni Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University
| | - Qinzhi Su
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University
| | - Xue Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University
| | - Chenyi Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University
| | - Shiqi Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University
| | - Xin Zhou
- College of Plant Protection, China Agricultural University
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University
| | - Hao Zheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University
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Moran NA, Ochman H, Hammer TJ. Evolutionary and ecological consequences of gut microbial communities. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019; 50:451-475. [PMID: 32733173 DOI: 10.1146/annurev-ecolsys-110617-062453] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Animals are distinguished by having guts: organs that must extract nutrients from food while barring invasion by pathogens. Most guts are colonized by non-pathogenic microorganisms, but the functions of these microbes, or even the reasons why they occur in the gut, vary widely among animals. Sometimes these microorganisms have co-diversified with hosts; sometimes they live mostly elsewhere in the environment. Either way, gut microorganisms often benefit hosts. Benefits may reflect evolutionary "addiction" whereby hosts incorporate gut microorganisms into normal developmental processes. But benefits often include novel ecological capabilities; for example, many metazoan clades exist by virtue of gut communities enabling new dietary niches. Animals vary immensely in their dependence on gut microorganisms, from lacking them entirely, to using them as food, to obligate dependence for development, nutrition, or protection. Many consequences of gut microorganisms for hosts can be ascribed to microbial community processes and the host's ability to shape these processes.
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Affiliation(s)
- Nancy A Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78703 USA
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78703 USA
| | - Tobin J Hammer
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78703 USA
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38
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Diversity of Wolbachia Associated with the Giant Turtle Ant, Cephalotes atratus. Curr Microbiol 2019; 76:1330-1337. [PMID: 31254009 DOI: 10.1007/s00284-019-01722-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/19/2019] [Indexed: 10/26/2022]
Abstract
Symbiotic relationships between organisms are common throughout the tree of life, and often these organisms share an evolutionary history. In turtle ants (Cephalotes), symbiotic associations with bacteria are known to be especially important for supplementing the nutrients that their herbivorous diets do not provide. However, much remains unknown about the diversity of many common bacterial symbionts with turtle ants, such as Wolbachia. Here, we surveyed the diversity of Wolbachia, focusing on one species of turtle ant with a particularly wide geographic range, Cephalotes atratus. Colonies were collected from the entire range of C. atratus, and we detected the presence of Wolbachia by sequencing multiple individuals per colony for wsp. Then, using the multilocus sequence typing (MLST) approach, we determined each individual's unique sequence type (ST) based on comparison to sequences published in the Wolbachia MLST Database ( https://pubmlst.org/wolbachia/ ). The results of this study suggest that there is a high level of diversity of Wolbachia strains among colonies from different regions, while the diversity within colonies is very low. Additionally, 13 novel variants (alleles) were uncovered. These results suggest that the level of diversity of Wolbachia within species is affected by geography, and the high level of diversity observed among Cephalotes atratus populations may be explained by their wide geographic range.
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39
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de Oliveira Junqueira AC, de Melo Pereira GV, Coral Medina JD, Alvear MCR, Rosero R, de Carvalho Neto DP, Enríquez HG, Soccol CR. First description of bacterial and fungal communities in Colombian coffee beans fermentation analysed using Illumina-based amplicon sequencing. Sci Rep 2019; 9:8794. [PMID: 31217528 PMCID: PMC6584692 DOI: 10.1038/s41598-019-45002-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 04/27/2019] [Indexed: 12/12/2022] Open
Abstract
In Colombia, coffee growers use a traditional method of fermentation to remove the cherry pulp surrounding the beans. This process has a great influence on sensory quality and prestige of Colombian coffee in international markets, but has never been studied. Here we use an Illumina-based amplicon sequencing to investigate bacterial and fungal communities associated with spontaneous coffee-bean fermentation in Colombia. Microbial-derived metabolites were further analysed by high-performance liquid chromatography and gas chromatography-mass spectrometry. Highly diverse bacterial groups, comprising 160 genera belonging to 10 phyla, were found. Lactic acid bacteria (LAB), mainly represented by the genera Leuconostoc and Lactobacillus, showed relative prevalence over 60% at all sampling times. The structure of the fungal community was more homogeneous, with Pichia nakasei dominating throughout the fermentation process. Lactic acid and acetaldehyde were the major end-metabolites produced by LAB and Pichia, respectively. In addition, 20 volatile compounds were produced, comprising alcohols, organic acids, aldehydes, esters, terpenes, phenols, and hydrocarbons. Interestingly, 56 microbial genera, associated with native soil, seawater, plants, insects, and human contact, were detected for the first time in coffee fermentation. These microbial groups harbour a remarkable phenotypic diversity and may impart flavours that yield clues to the terroir of Colombian coffees.
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Affiliation(s)
- Ana C de Oliveira Junqueira
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná, 81531-980, Brazil
| | - Gilberto V de Melo Pereira
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná, 81531-980, Brazil
| | - Jesus D Coral Medina
- Department of Process and Biotechnology, Mariana University, 520002, Pasto, Nariño, Colombia
| | - María C R Alvear
- Department of Process and Biotechnology, Mariana University, 520002, Pasto, Nariño, Colombia
| | - Rubens Rosero
- Department of Process and Biotechnology, Mariana University, 520002, Pasto, Nariño, Colombia
| | - Dão P de Carvalho Neto
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná, 81531-980, Brazil
| | - Hugo G Enríquez
- Department of Process and Biotechnology, Mariana University, 520002, Pasto, Nariño, Colombia
| | - Carlos R Soccol
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná, 81531-980, Brazil.
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40
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Ribeiro LF, Solar RRC, Sobrinho TG, Muscardi DC, Schoereder JH, Andersen AN. Different trophic groups of arboreal ants show differential responses to resource supplementation in a neotropical savanna. Oecologia 2019; 190:433-443. [PMID: 31069514 DOI: 10.1007/s00442-019-04414-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 04/30/2019] [Indexed: 11/30/2022]
Abstract
Resource-ratio theory predicts that consumers should achieve optimal ratios of complementary nutrients. Accordingly, different trophic groups are expected to vary in their N-limitation depending on the extent to which they feed primarily on carbohydrate (CHO) or protein. Among arboreal ants, N-limitation ranges from high (for trophobiont tenders), intermediate (leaf foragers) and low (predators). We report results from a manipulative field experiment in a Brazilian savanna that tests the differential attractiveness of nitrogen and CHO to arboreal ants, as well as experimentally examines changes in broader ant foraging patterns in response to protein and CHO supplementation. Every tree within 32 20 × 20 m plots were supplemented with either protein, CHO; protein + CHO or a water control (n = 8 in each case) for a 7-day period in each of the wet and dry seasons. As predicted, different trophic groups responded differentially to supplementation treatment according to the extent of their N-limitation. The richness and abundance of the most N-limited group (trophobiont tenders) was highest at protein supplements, whereas less N-limited trophic groups showed highest species richness (leaf foragers) or abundance (predators) at CHO supplements. Protein supplementation markedly increased the general foraging abundance of trophobiont tenders, but decreased the abundance of leaf foragers. We attribute the latter to increased competition from behaviorally dominant trophobiont tenders. Our study provides experimental evidence that nutrient availability is a major factor influencing arboreal ant communities, both directly through the provision of different resources, and indirectly through increased competitive pressure.
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Affiliation(s)
- Laila F Ribeiro
- Programa de Pós-Graduação em Entomologia, Universidade Federal de Viçosa, Avenida P.H. Rolfs, s/n, Campus Universitário, Viçosa, MG, CEP 36570-000, Brazil.
| | - Ricardo R C Solar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Pres. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, CEP 31270-901, Brazil
| | - Tathiana G Sobrinho
- Departamento de Ciências Agrárias e Biológicas, Universidade Federal do Espírito Santo, BR 101 Norte, Km 60, São Mateus, ES, CEP 29932-540, Brazil
| | - Dalana C Muscardi
- Departamento de Educação e Ciências Humanas, Universidade Federal do Espírito Santo, BR 101 Norte, Km 60, São Mateus, ES, CEP 29932-540, Brazil
| | - José H Schoereder
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Avenida P.H. Rolfs, s/n, Campus Universitário, Viçosa, MG, CEP 36570-000, Brazil
| | - Alan N Andersen
- Research School for the Environment and Livelihoods, Charles Darwin University, Casuarina, NT, 0909, Australia
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41
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Lane AA, McGuire MK, McGuire MA, Williams JE, Lackey KA, Hagen EH, Kaul A, Gindola D, Gebeyehu D, Flores KE, Foster JA, Sellen DW, Kamau-Mbuthia EW, Kamundia EW, Mbugua S, Moore SE, Prentice AM, Kvist LJ, Otoo GE, Rodríguez JM, Ruiz L, Pareja RG, Bode L, Price WJ, Meehan CL. Household composition and the infant fecal microbiome: The INSPIRE study. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 169:526-539. [PMID: 31012086 DOI: 10.1002/ajpa.23843] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/01/2019] [Accepted: 04/07/2019] [Indexed: 12/18/2022]
Abstract
OBJECTIVES Establishment and development of the infant gastrointestinal microbiome (GIM) varies cross-culturally and is thought to be influenced by factors such as gestational age, birth mode, diet, and antibiotic exposure. However, there is little data as to how the composition of infants' households may play a role, particularly from a cross-cultural perspective. Here, we examined relationships between infant fecal microbiome (IFM) diversity/composition and infants' household size, number of siblings, and number of other household members. MATERIALS AND METHODS We analyzed 377 fecal samples from healthy, breastfeeding infants across 11 sites in eight different countries (Ethiopia, The Gambia, Ghana, Kenya, Peru, Spain, Sweden, and the United States). Fecal microbial community structure was determined by amplifying, sequencing, and classifying (to the genus level) the V1-V3 region of the bacterial 16S rRNA gene. Surveys administered to infants' mothers identified household members and composition. RESULTS Our results indicated that household composition (represented by the number of cohabitating siblings and other household members) did not have a measurable impact on the bacterial diversity, evenness, or richness of the IFM. However, we observed that variation in household composition categories did correspond to differential relative abundances of specific taxa, namely: Lactobacillus, Clostridium, Enterobacter, and Klebsiella. DISCUSSION This study, to our knowledge, is the largest cross-cultural study to date examining the association between household composition and the IFM. Our results indicate that the social environment of infants (represented here by the proxy of household composition) may influence the bacterial composition of the infant GIM, although the mechanism is unknown. A higher number and diversity of cohabitants and potential caregivers may facilitate social transmission of beneficial bacteria to the infant gastrointestinal tract, by way of shared environment or through direct physical and social contact between the maternal-infant dyad and other household members. These findings contribute to the discussion concerning ways by which infants are influenced by their social environments and add further dimensionality to the ongoing exploration of social transmission of gut microbiota and the "old friends" hypothesis.
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Affiliation(s)
- Avery A Lane
- Department of Anthropology, Washington State University, Pullman, Washington
| | - Michelle K McGuire
- School of Family and Consumer Sciences, University of Idaho, Moscow, Idaho
| | - Mark A McGuire
- Department of Animal and Veterinary Science, University of Idaho, Moscow, Idaho
| | - Janet E Williams
- Department of Animal and Veterinary Science, University of Idaho, Moscow, Idaho
| | - Kimberly A Lackey
- School of Family and Consumer Sciences, University of Idaho, Moscow, Idaho
| | - Edward H Hagen
- Department of Anthropology, Washington State University, Pullman, Washington
| | - Abhishek Kaul
- Department of Mathematics and Statistics, Washington State University, Pullman, Washington
| | - Debela Gindola
- Department of Anthropology, Hawassa University, Hawassa, Ethiopia
| | - Dubale Gebeyehu
- Department of Anthropology, Hawassa University, Hawassa, Ethiopia
| | - Katherine E Flores
- Department of Anthropology, Washington State University, Pullman, Washington
| | - James A Foster
- Department of Biological Sciences, University of Idaho, Moscow, Idaho
| | - Daniel W Sellen
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Samwel Mbugua
- Department of Human Nutrition, Egerton University, Nakuru, Kenya
| | - Sophie E Moore
- Department of Women and Children's Health, King's College London, London, United Kingdom.,MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Andrew M Prentice
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia.,MRC International Nutrition Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Gloria E Otoo
- Department of Nutrition and Food Science, University of Ghana, Accra, Ghana
| | - Juan M Rodríguez
- Department of Nutrition and Food Science, Complutense University of Madrid, Madrid, Spain
| | - Lorena Ruiz
- Department of Nutrition and Food Science, Complutense University of Madrid, Madrid, Spain.,Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas, Villaviciosa, Spain
| | | | - Lars Bode
- Department of Pediatrics, and Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California, San Diego, California
| | - William J Price
- Statistical Programs, College of Agriculture and Life Sciences, University of Idaho, Moscow, Idaho
| | - Courtney L Meehan
- Department of Anthropology, Washington State University, Pullman, Washington
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Szenteczki MA, Pitteloud C, Casacci LP, Kešnerová L, Whitaker MR, Engel P, Vila R, Alvarez N. Bacterial communities within Phengaris (Maculinea) alcon caterpillars are shifted following transition from solitary living to social parasitism of Myrmica ant colonies. Ecol Evol 2019; 9:4452-4464. [PMID: 31031919 PMCID: PMC6476763 DOI: 10.1002/ece3.5010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/30/2019] [Accepted: 02/01/2019] [Indexed: 02/01/2023] Open
Abstract
Bacterial symbionts are known to facilitate a wide range of physiological processes and ecological interactions for their hosts. In spite of this, caterpillars with highly diverse life histories appear to lack resident microbiota. Gut physiology, endogenous digestive enzymes, and limited social interactions may contribute to this pattern, but the consequences of shifts in social activity and diet on caterpillar microbiota are largely unknown. Phengaris alcon caterpillars undergo particularly dramatic social and dietary shifts when they parasitize Myrmica ant colonies, rapidly transitioning from solitary herbivory to ant tending (i.e., receiving protein-rich regurgitations through trophallaxis). This unique life history provides a model for studying interactions between social living, diet, and caterpillar microbiota. Here, we characterized and compared bacterial communities within P. alcon caterpillars before and after their association with ants, using 16S rRNA amplicon sequencing and quantitative PCR. After being adopted by ants, bacterial communities within P. alcon caterpillars shifted substantially, with a significant increase in alpha diversity and greater consistency in bacterial community composition in terms of beta dissimilarity. We also characterized the bacterial communities within their host ants (Myrmica schencki), food plant (Gentiana cruciata), and soil from ant nest chambers. These data indicated that the aforementioned patterns were influenced by bacteria derived from caterpillars' surrounding environments, rather than through transfers from ants. Thus, while bacterial communities are substantially reorganized over the life cycle of P. alcon caterpillars, it appears that they do not rely on transfers of bacteria from host ants to complete their development.
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Affiliation(s)
- Mark A. Szenteczki
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Camille Pitteloud
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Present address:
Department of Environmental Systems SciencesInstitute of Terrestrial Ecosystems, ETHZZürichSwitzerland
| | - Luca P. Casacci
- Museum and Institute of ZoologyPolish Academy of SciencesWarsawPoland
- Department of Life Sciences and Systems BiologyUniversity of TurinTurinItaly
| | - Lucie Kešnerová
- Department of Fundamental MicrobiologyUniversity of LausanneSwitzerland
| | | | - Philipp Engel
- Department of Fundamental MicrobiologyUniversity of LausanneSwitzerland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC‐UPF)BarcelonaSpain
| | - Nadir Alvarez
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Unit of Research and CollectionsMuseum of Natural HistoryGenevaSwitzerland
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Barak H, Kumar P, Zaritsky A, Mendel Z, Ment D, Kushmaro A, Ben-Dov E. Diversity of Bacterial Biota in Capnodis tenebrionis (Coleoptera: Buprestidae) Larvae. Pathogens 2019; 8:E4. [PMID: 30621355 PMCID: PMC6470736 DOI: 10.3390/pathogens8010004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 01/01/2019] [Accepted: 01/04/2019] [Indexed: 11/17/2022] Open
Abstract
The bacterial biota in larvae of Capnodis tenebrionis, a serious pest of cultivated stone-fruit trees in the West Palearctic, was revealed for the first time using the MiSeq platform. The core bacterial community remained the same in neonates whether upon hatching or grown on peach plants or an artificial diet, suggesting that C. tenebrionis larvae acquire much of their bacterial biome from the parent adult. Reads affiliated with class levels Gammaproteobacteria and Alphaproteobacteria (phylum Proteobacteria ca. 86%), and Actinobacteria (ca. 14%) were highly abundant. Most diverse reads belong to the families Xanthomonadaceae (50%), Methylobacteriaceae (20%), Hyphomicrobiaceae (9%), Micrococcaceae (7%) and Geodermatophilaceae (4.5%). About two-thirds of the reads are affiliated with the genera Lysobacter, Microvirga, Methylobacterium, and Arthrobacter, which encompass species displaying cellulolytic and lipolytic activities. This study provides a foundation for future studies to elucidate the roles of bacterial biota in C. tenebrionis.
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Affiliation(s)
- Hana Barak
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel.
| | - Pradeep Kumar
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel.
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel.
| | - Arieh Zaritsky
- Faculty of Natural Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel.
| | - Zvi Mendel
- Department of Entomology, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel.
| | - Dana Ment
- Department of Entomology, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel.
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel.
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.
| | - Eitan Ben-Dov
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel.
- Department of Life Sciences, Achva Academic College, M.P. Shikmim Arugot 7980400, Israel.
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44
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Sapountzis P, Nash DR, Schiøtt M, Boomsma JJ. The evolution of abdominal microbiomes in fungus-growing ants. Mol Ecol 2018; 28:879-899. [PMID: 30411820 PMCID: PMC6446810 DOI: 10.1111/mec.14931] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/08/2018] [Accepted: 10/03/2018] [Indexed: 01/01/2023]
Abstract
The attine ants are a monophyletic lineage that switched to fungus farming ca. 55-60 MYA. They have become a model for the study of complex symbioses after additional fungal and bacterial symbionts were discovered, but their abdominal endosymbiotic bacteria remain largely unknown. Here, we present a comparative microbiome analysis of endosymbiotic bacteria spanning the entire phylogenetic tree. We show that, across 17 representative sympatric species from eight genera sampled in Panama, abdominal microbiomes are dominated by Mollicutes, α- and γ-Proteobacteria, and Actinobacteria. Bacterial abundances increase from basal to crown branches in the phylogeny reflecting a shift towards putative specialized and abundant abdominal microbiota after the ants domesticated gongylidia-bearing cultivars, but before the origin of industrial-scale farming based on leaf-cutting herbivory. This transition coincided with the ancestral single colonization event of Central/North America ca. 20 MYA, documented in a recent phylogenomic study showing that almost the entire crown group of the higher attine ants, including the leaf-cutting ants, evolved there and not in South America. Several bacterial species are located in gut tissues or abdominal organs of the evolutionarily derived, but not the basal attine ants. The composition of abdominal microbiomes appears to be affected by the presence/absence of defensive antibiotic-producing actinobacterial biofilms on the worker ants' cuticle, but the significance of this association remains unclear. The patterns of diversity, abundance and sensitivity of the abdominal microbiomes that we obtained explore novel territory in the comparative analysis of attine fungus farming symbioses and raise new questions for further in-depth research.
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Affiliation(s)
- Panagiotis Sapountzis
- Centre for Social Evolution, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - David R Nash
- Centre for Social Evolution, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Morten Schiøtt
- Centre for Social Evolution, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
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45
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Bisch G, Neuvonen MM, Pierce NE, Russell JA, Koga R, Sanders JG, Lukasik P, Andersson SGE. Genome Evolution of Bartonellaceae Symbionts of Ants at the Opposite Ends of the Trophic Scale. Genome Biol Evol 2018; 10:1687-1704. [PMID: 29982531 PMCID: PMC6044324 DOI: 10.1093/gbe/evy126] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2018] [Indexed: 12/17/2022] Open
Abstract
Many insects rely on bacterial symbionts to supply essential amino acids and vitamins that are deficient in their diets, but metabolic comparisons of closely related gut bacteria in insects with different dietary preferences have not been performed. Here, we demonstrate that herbivorous ants of the genus Dolichoderus from the Peruvian Amazon host bacteria of the family Bartonellaceae, known for establishing chronic or pathogenic infections in mammals. We detected these bacteria in all studied Dolichoderus species, and found that they reside in the midgut wall, that is, the same location as many previously described nutritional endosymbionts of insects. The genomic analysis of four divergent strains infecting different Dolichoderus species revealed genes encoding pathways for nitrogen recycling and biosynthesis of several vitamins and all essential amino acids. In contrast, several biosynthetic pathways have been lost, whereas genes for the import and conversion of histidine and arginine to glutamine have been retained in the genome of a closely related gut bacterium of the carnivorous ant Harpegnathos saltator. The broad biosynthetic repertoire in Bartonellaceae of herbivorous ants resembled that of gut bacteria of honeybees that likewise feed on carbohydrate-rich diets. Taken together, the broad distribution of Bartonellaceae across Dolichoderus ants, their small genome sizes, the specific location within hosts, and the broad biosynthetic capability suggest that these bacteria are nutritional symbionts in herbivorous ants. The results highlight the important role of the host nutritional biology for the genomic evolution of the gut microbiota-and conversely, the importance of the microbiota for the nutrition of hosts.
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Affiliation(s)
- Gaelle Bisch
- Cell and Molecular Biology, Science for Life Laboratory, Department of Molecular Evolution, Uppsala University, Sweden
| | - Minna-Maria Neuvonen
- Cell and Molecular Biology, Science for Life Laboratory, Department of Molecular Evolution, Uppsala University, Sweden
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University
| | | | - Ryuichi Koga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Jon G Sanders
- Department of Organismic and Evolutionary Biology, Harvard University.,Department of Pediatrics, University of California San Diego, La Jolla
| | - Piotr Lukasik
- Department of Biology, Drexel University.,Division of Biological Sciences, University of Montana
| | - Siv G E Andersson
- Cell and Molecular Biology, Science for Life Laboratory, Department of Molecular Evolution, Uppsala University, Sweden
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46
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Hubert J, Nesvorna M, Sopko B, Smrz J, Klimov P, Erban T. Two Populations of Mites ( Tyrophagus putrescentiae) Differ in Response to Feeding on Feces-Containing Diets. Front Microbiol 2018; 9:2590. [PMID: 30425700 PMCID: PMC6218854 DOI: 10.3389/fmicb.2018.02590] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/10/2018] [Indexed: 01/08/2023] Open
Abstract
Background:Tyrophagus putrescentiae is a ubiquitous mite species in soil, stored products and house dust and infests food and causes allergies in people. T. putrescentiae populations harbor different bacterial communities, including intracellular symbionts and gut bacteria. The spread of microorganisms via the fecal pellets of T. putrescentiae is a possibility that has not been studied in detail but may be an important means by which gut bacteria colonize subsequent generations of mites. Feces in soil may be a vector for the spread of microorganisms. Methods: Extracts from used mite culture medium (i.e., residual food, mite feces, and dead mite bodies) were used as a source of feces-inhabiting microorganisms as food for the mites. Two T. putrescentiae populations (L and P) were used for experiments, and they hosted the intracellular bacteria Cardinium and Wolbachia, respectively. The effects of the fecal fraction on respiration in a mite microcosm, mite nutrient contents, population growth and microbiome composition were evaluated. Results: Feces from the P population comprised more than 90% Bartonella-like sequences. Feces from the L population feces hosted Staphylococcus, Virgibacillus, Brevibacterium, Enterobacteriaceae, and Bacillus. The mites from the P population, but not the L population, exhibited increased bacterial respiration in the microcosms in comparison to no-mite controls. Both L- and P-feces extracts had an inhibitory effect on the respiration of the microcosms, indicating antagonistic interactions within feces-associated bacteria. The mite microbiomes were resistant to the acquisition of new bacterial species from the feces, but their bacterial profiles were affected. Feeding of P mites on P-feces-enriched diets resulted in an increase in Bartonella abundance from 6 to 20% of the total bacterial sequences and a decrease in Bacillus abundance. The population growth was fivefold accelerated on P-feces extracts in comparison to the control. Conclusion: The mite microbiome, to a certain extent, resists the acquisition of new bacteria when mites are fed on feces of the same species. However, a Bartonella-like bacteria-feces-enriched diet seems to be beneficial for mite populations with symbiotic Bartonella-like bacteria. Coprophagy on the feces of its own population may be a mechanism of bacterial acquisition in T. putrescentiae.
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Affiliation(s)
- Jan Hubert
- Divison of Crop Protection and Plant Health, Crop Research Institute, Prague, Czechia
| | - Marta Nesvorna
- Divison of Crop Protection and Plant Health, Crop Research Institute, Prague, Czechia
| | - Bruno Sopko
- Divison of Crop Protection and Plant Health, Crop Research Institute, Prague, Czechia.,Department of Medical Chemistry and Clinical Biochemistry, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czechia
| | - Jaroslav Smrz
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Pavel Klimov
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States.,Institute of Biology, University of Tyumen, Tyumen, Russia
| | - Tomas Erban
- Divison of Crop Protection and Plant Health, Crop Research Institute, Prague, Czechia
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47
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Lester PJ, Sébastien A, Suarez AV, Barbieri RF, Gruber MAM. Symbiotic bacterial communities in ants are modified by invasion pathway bottlenecks and alter host behavior. Ecology 2018; 98:861-874. [PMID: 28039867 DOI: 10.1002/ecy.1714] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 12/13/2016] [Accepted: 12/29/2016] [Indexed: 01/06/2023]
Abstract
Biological invasions are a threat to global biodiversity and provide unique opportunities to study ecological processes. Population bottlenecks are a common feature of biological invasions and the severity of these bottlenecks is likely to be compounded as an invasive species spreads from initial invasion sites to additional locations. Despite extensive work on the genetic consequences of bottlenecks, we know little about how they influence microbial communities of the invaders themselves. Due to serial bottlenecks, invasive species may lose microbial symbionts including pathogenic taxa (the enemy release hypothesis) and/or may accumulate natural enemies with increasing time after invasion (the pathogen accumulation and invasive decline hypothesis). We tested these alternate hypotheses by surveying bacterial communities of Argentine ants (Linepithema humile). We found evidence for serial symbiont bottlenecks: the bacterial community richness declined over the invasion pathway from Argentina to New Zealand. The abundance of some genera, such as Lactobacillus, also significantly declined over the invasion pathway. Argentine ants from populations in the United States shared the most genera with ants from their native range in Argentina, while New Zealand shared the least (120 vs. 57, respectively). Nine genera were present in all sites around the globe possibly indicating a core group of obligate microbes. In accordance with the pathogen accumulation and invasive decline hypothesis, Argentine ants acquired genera unique to each specific invaded country. The United States had the most unique genera, though even within New Zealand these ants acquired symbionts. In addition to our biogeographic sampling, we administered antibiotics to Argentine ants to determine if changes in the micro-symbiont community could influence behavior and survival in interspecific interactions. Treatment with the antibiotics spectinomycin and kanamycin only slightly increased Argentine ant interspecific aggression, but this increase significantly decreased survival in interspecific interactions. The survival of the native ant species also decreased when the symbiotic microbial community within Argentine ants was modified by antibiotics. Our work offers support for both the enemy release hypothesis and that invasive species accumulate novel microbial taxa within their invaded range. These changes appear likely to influence invader behavior and survival.
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Affiliation(s)
- Philip J Lester
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Alexandra Sébastien
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Andrew V Suarez
- Department of Animal Biology, University of Illinois, Urbana, Illinois, 61801, USA
| | - Rafael F Barbieri
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Monica A M Gruber
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
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48
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van Schooten B, Godoy-Vitorino F, McMillan WO, Papa R. Conserved microbiota among young Heliconius butterfly species. PeerJ 2018; 6:e5502. [PMID: 30310733 PMCID: PMC6173163 DOI: 10.7717/peerj.5502] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 08/01/2018] [Indexed: 12/03/2022] Open
Abstract
Background Insects are the most diverse group of animals which have established intricate evolutionary interactions with bacteria. However, the importance of these interactions is still poorly understood. Few studies have focused on a closely related group of insect species, to test the similarities and differences between their microbiota. Heliconius butterflies are a charismatic recent insect radiation that evolved the unique ability to use pollen as a protein source, which affected life history traits and resulted in an elevated speciation rates. We hypothesize that different Heliconius butterflies sharing a similar trophic pollen niche, harbor a similar gut flora within species, population and sexes. Methods To test our hypothesis, we characterized the microbiota of 38 adult male and female butterflies representing six species of Heliconius butterflies and 2 populations of the same species. We sequenced the V4 region of the 16S rRNA gene with the Roche 454 system and analyzed the data with standard tools for microbiome analysis. Results Overall, we found a low microbial diversity with only 10 OTUs dominating across all individuals, mostly Proteobacteria and Firmicutes, which accounted for 99.5% of the bacterial reads. When rare reads were considered, we identified a total of 406 OTUs across our samples. We identified reads within Phyla Chlamydiae, found in 5 butterflies of four species. Interestingly, only three OTUs were shared among all 38 individuals (Bacillus, Enterococcus and Enterobacteriaceae). Altogether, the high individual variation overshadowed species and sex differences. Thus, bacterial communities were not structured randomly with 13% of beta-diversity explained by species, and 40 rare OTUs being significantly different across species. Finally, 13 OTUs, including the intercellular symbiont Spiroplasma, varied significantly in relative abundance between males and females. Discussion The Heliconius microbial communities in these 38 individuals show a low diversity with few differences in the rare microbes between females, males, species or populations. Indeed, Heliconius butterflies, similarly to other insects, are dominated by few OTUs, mainly from Proteobacteria and Firmicutes. The overall low microbial diversity observed contrasts with the high intra-species variation in microbiome composition. This could indicate that much of the microbiome maybe acquired from their surroundings. The significant differences between species and sexes were restricted to rare taxa, which could be important for microbial community stability under changing conditions as seen in other host-microbiome systems. The presence of symbionts like Spiroplasma or Chlamydiae, identified in this study for the first time in Heliconius, could play a vital role in their behavior and evolution by vertical transmission. Altogether, our study represents a step forward into the description of the microbial diversity in a charismatic group of closely related butterflies.
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Affiliation(s)
- Bas van Schooten
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico
| | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, School of Medicine, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | | | - Riccardo Papa
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico.,Smithsonian Tropical Research Institute, Panamá, Panama.,University of Puerto Rico, Molecular Sciences and Research Center, San Juan, Puerto Rico
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49
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Rubin BER, Kautz S, Wray BD, Moreau CS. Dietary specialization in mutualistic acacia-ants affects relative abundance but not identity of host-associated bacteria. Mol Ecol 2018; 28:900-916. [PMID: 30106217 DOI: 10.1111/mec.14834] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 07/18/2018] [Accepted: 07/30/2018] [Indexed: 12/17/2022]
Abstract
Acacia-ant mutualists in the genus Pseudomyrmex nest obligately in acacia plants and, as we show through stable isotope analysis, feed at a remarkably low trophic level. Insects with diets such as these sometimes depend on bacterial symbionts for nutritional enrichment. We, therefore, examine the bacterial communities associated with acacia-ants in order to determine whether they host bacterial partners likely to contribute to their nutrition. Despite large differences in trophic position, acacia-ants and related species with generalized diets do not host distinct bacterial taxa. However, we find that a small number of previously undescribed bacterial taxa do differ in relative abundance between acacia-ants and generalists, including several Acetobacteraceae and Nocardiaceae lineages related to common insect associates. Comparisons with an herbivorous generalist, a parasite that feeds on acacias and a mutualistic species with a generalized diet show that trophic level is likely responsible for these small differences in bacterial community structure. While we did not experimentally test for a nutritional benefit to hosts of these bacterial lineages, metagenomic analysis reveals a Bartonella relative with an intact nitrogen-recycling pathway widespread across Pseudomyrmex mutualists and generalists. This taxon may be contributing to nitrogen enrichment of its ant hosts through urease activity and, concordant with an obligately host-associated lifestyle, appears to be experiencing genomewide relaxed selection. The lack of distinctiveness in bacterial communities across trophic level in this group of ants shows a remarkable ability to adjust to varied diets, possibly with assistance from these diverse ant-specific bacterial lineages.
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Affiliation(s)
- Benjamin E R Rubin
- Department of Science and Education, Field Museum of Natural History, Chicago, Illinois
| | - Stefanie Kautz
- Department of Biology, Portland State University, Portland, Oregon
| | - Brian D Wray
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Corrie S Moreau
- Department of Science and Education, Field Museum of Natural History, Chicago, Illinois
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50
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Mohr KI. Diversity of Myxobacteria-We Only See the Tip of the Iceberg. Microorganisms 2018; 6:E84. [PMID: 30103481 PMCID: PMC6164225 DOI: 10.3390/microorganisms6030084] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 11/20/2022] Open
Abstract
The discovery of new antibiotics is mandatory with regard to the increasing number of resistant pathogens. One approach is the search for new antibiotic producers in nature. Among actinomycetes, Bacillus species, and fungi, myxobacteria have been a rich source for bioactive secondary metabolites for decades. To date, about 600 substances could be described, many of them with antibacterial, antifungal, or cytostatic activity. But, recent cultivation-independent studies on marine, terrestrial, or uncommon habitats unequivocally demonstrate that the number of uncultured myxobacteria is much higher than would be expected from the number of cultivated strains. Although several highly promising myxobacterial taxa have been identified recently, this so-called Great Plate Count Anomaly must be overcome to get broader access to new secondary metabolite producers. In the last years it turned out that especially new species, genera, and families of myxobacteria are promising sources for new bioactive metabolites. Therefore, the cultivation of the hitherto uncultivable ones is our biggest challenge.
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Affiliation(s)
- Kathrin I Mohr
- Microbial Drugs (MWIS), Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany.
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