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You M, Yang W. Environmental Changes Driving Shifts in the Structure and Functional Properties of the Symbiotic Microbiota of Daphnia. Microorganisms 2024; 12:2492. [PMID: 39770695 PMCID: PMC11728151 DOI: 10.3390/microorganisms12122492] [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: 11/11/2024] [Revised: 11/29/2024] [Accepted: 12/02/2024] [Indexed: 01/16/2025] Open
Abstract
Symbiotic microbiota significantly influence the development, physiology, and behavior of their hosts, and therefore, they are widely studied. However, very few studies have investigated the changes in symbiotic microbiota across generations. Daphnia magna originating from the Qinghai-Tibetan Plateau were cultured through seven generations in our laboratory, and the symbiotic microbiota of D. magna were sequenced using a 16S rRNA amplicon to analyze changes in the structure and functional properties of the symbiotic microbiota of D. magna from a harsh environment to an ideal environment. We detected substantial changes in the symbiotic microbiota of D. magna across generations. For example, the genus Nevskia, a member of the gamma-subclass Proteobacteria, had the highest abundance in the first generation (G1), followed by a decrease in abundance in the fourth (G4) and seventh (G7) generations. The gene functions of the microbiota in different generations of D. magna also changed significantly. The fourth generation was mainly rich in fatty acyl-CoA synthase, acetyl-CoA acyltransferase, phosphoglycerol phosphatase, etc. The seventh generation was mainly rich in osmotic enzyme protein and ATP-binding protein of the ABC transport system. This study confirms that the alterations in the structure and functional properties of the symbiotic microbiota of D. magna under changing environments are typical responses of D. magna to environmental changes.
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Affiliation(s)
| | - Wenwu Yang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai 200438, China;
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2
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Rajarajan A, Decaestecker E, Bulteel L, Walser JC, Spaak P, Wolinska J. Host genotype and infection status interact to shape microbiomes in Daphnia magna. Parasitology 2024:1-11. [PMID: 39542865 DOI: 10.1017/s0031182024000787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2024]
Abstract
Host–bacterial communities (microbiomes) are influenced by a wide range of factors including host genotype and parasite exposure. However, few studies disentangle temporal and host-genotype-specific variation in microbiome response to infection across several host tissues. We experimentally exposed the freshwater crustacean Daphnia magna to its fungal parasite Metschnikowia bicuspidata and characterized changes in host–bacterial communities associated with the parasite's development within the host. We used 16S rRNA gene sequencing to assess bacterial communities of the host (a) 24 h (‘initial parasite exposure’) and (b) 10 days (‘successful infection’) after exposure to a standard dose of M. bicuspidata spores, in host guts, body tissue (excluding guts) and whole individuals. We also investigated whether bacterial community responses to parasite exposure varied by host genotype.Parasite exposure did not immediately alter host gut bacterial communities, but drove host-genotype-specific changes in the bacterial community composition of whole individuals. We validated that these changes were not driven by shifts in bacterial communities of the culturing medium, due to the addition of the parasite spore solution. Successful infection (i.e. the proliferation of M. bicuspidata spores in the host body) reduced alpha diversity and shifted abundance of dominant bacterial orders in the gut. Moreover, it induced a host-genotype-specific changes in body bacterial community composition. Overall, bacterial community responses to parasite exposure and subsequent infection are complex: they occur in a host-genotype-dependent manner, differentially at distinct timepoints after parasite exposure, and in specific host tissue.
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Affiliation(s)
- Amruta Rajarajan
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag) Dübendorf, Zürich, Switzerland
- Dept. of Evolutionary and Integrative Ecology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Ellen Decaestecker
- Dept. of Ecology, Evolution and Biodiversity Conservation, University of Leuven, Campus-Kulak, Kortrijk, Belgium
| | - Lore Bulteel
- Dept. of Ecology, Evolution and Biodiversity Conservation, University of Leuven, Campus-Kulak, Kortrijk, Belgium
| | - Jean-Claude Walser
- Genetic Diversity Centre, Dept. of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Piet Spaak
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag) Dübendorf, Zürich, Switzerland
| | - Justyna Wolinska
- Dept. of Evolutionary and Integrative Ecology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, Berlin, Germany
- Dept. of Biology, Chemistry and Pharmacy, Freie Universität (FU) Berlin, Berlin, Germany
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3
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Shahmohamadloo RS, Gabidulin AR, Andrews ER, Fryxell JM, Rudman SM. A test for microbiome-mediated rescue via host phenotypic plasticity in Daphnia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.14.607994. [PMID: 39185203 PMCID: PMC11343196 DOI: 10.1101/2024.08.14.607994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Phenotypic plasticity is a primary mechanism by which organismal phenotypes shift in response to the environment. Host-associated microbiomes often exhibit considerable shifts in response to environmental variation and these shifts could facilitate host phenotypic plasticity, adaptation, or rescue populations from extinction. However, it is unclear how much shifts in microbiome composition contribute to host phenotypic plasticity, limiting our knowledge of the underlying mechanisms of plasticity and, ultimately, the fate of populations inhabiting changing environments. In this study, we examined phenotypic responses and microbiome composition in 20 genetically distinct Daphnia magna clones exposed to non-toxic and toxic diets containing Microcystis, a cosmopolitan cyanobacteria and common stressor for Daphnia. Daphnia exhibited significant plasticity in survival, reproduction, and population growth rates in response to Microcystis exposure. However, the effects of Microcystis exposure on the Daphnia microbiome were limited, with the primary effect being differences in abundance observed across five bacterial families. Moreover, there was no significant correlation between the magnitude of microbiome shifts and host phenotypic plasticity. Our results suggest that microbiome composition played a negligible role in driving host phenotypic plasticity or microbiome-mediated rescue.
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Affiliation(s)
- René S. Shahmohamadloo
- School of Biological Sciences, Washington State University, Vancouver, WA, United States
| | - Amir R. Gabidulin
- School of Biological Sciences, Washington State University, Vancouver, WA, United States
| | - Ellie R. Andrews
- School of Biological Sciences, Washington State University, Vancouver, WA, United States
| | - John M. Fryxell
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Seth M. Rudman
- School of Biological Sciences, Washington State University, Vancouver, WA, United States
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4
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Lydy VR, Regn OZ, Bouldin JL. Toxicant Responses and Culturing Characteristics of Long-Term Laboratory-Reared and Field Populations of Ceriodaphnia dubia. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024; 43:159-169. [PMID: 37861383 DOI: 10.1002/etc.5772] [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: 06/29/2023] [Revised: 07/26/2023] [Accepted: 10/17/2023] [Indexed: 10/21/2023]
Abstract
Ceriodaphnia dubia is a standardized test organism for regulatory toxicity testing of surface waters and commercial chemicals because of its simplicity to culture and responsiveness to toxicants. For testing convenience, C. dubia is often cultured for extended periods in the laboratory with little knowledge of the impact on subsequent generations. Extended laboratory rearing could impact how they respond to stressors and decrease the accuracy of test results. The present study investigated if C. dubia cultured for an extended period were representative of three recently collected field populations by comparing their culturing characteristics and sensitivities to toxicants. For culturing characteristics, the field cultures were more challenging because they had shorter body lengths, fewer neonates, and higher mortality rates than the laboratory culture. Comparative chronic toxicity tests with sodium chloride and the neonicotinoid insecticide thiamethoxam indicated that the laboratory and field organisms did not differ much in their toxicological responses but did differ in the variability of responses (percentage of coefficient of variation). The differences between the laboratory and field cultures found in the present study highlight the challenges of addressing discrepancies between laboratory and field applications in existing standardized methodologies. Environ Toxicol Chem 2024;43:159-169. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Victoria R Lydy
- Ecotoxicology Research Facility, Arkansas State University, Jonesboro, Arkansas, USA
| | - Orithea Z Regn
- Ecotoxicology Research Facility, Arkansas State University, Jonesboro, Arkansas, USA
| | - Jennifer L Bouldin
- Ecotoxicology Research Facility, Arkansas State University, Jonesboro, Arkansas, USA
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5
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Houwenhuyse S, Callens M, Bulteel L, Decaestecker E. Comparison between the gut bacterial community of laboratory cultured and wild Daphnia. FEMS Microbiol Ecol 2023; 99:fiad116. [PMID: 37740575 DOI: 10.1093/femsec/fiad116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 09/24/2023] Open
Abstract
The fitness of an organism is often impacted by the composition and biological activity of its associated bacterial community. Many factors, including host genetics, diet, and temperature can influence the bacterial community composition. Furthermore, these factors can differ strongly between natural and laboratory environments. Consequently, several studies have highlighted results from laboratory experiments investigating host-associated bacterial communities to be conflicting with those obtained under field conditions. Here, we compared the Daphnia magna gut bacterial communities in natural host populations with those of laboratory cultured hosts. We further analyzed changes in the gut bacterial communities after transferring hosts from natural populations to the laboratory on the short- and long-term. Results show that, in general, the gut bacterial communities from natural populations differ from those of laboratory cultures and that their composition and diversity changed one hour after being transferred to the laboratory. Over the following 14 days, the composition and diversity changed gradually. On the longer term (after two years of rearing hosts in the laboratory) the composition and diversity of the gut bacterial communities was strongly altered compared to the initial state. Our findings indicate that the gut bacterial communities of Daphnia magna in laboratory experiments is not representative for natural field conditions, and that caution should be taken when interpreting results from laboratory experiments for natural settings.
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Affiliation(s)
- Shira Houwenhuyse
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven- KU Leuven, Campus KULAK, E. Sabbelaan 53, 8500 Kortrijk, Belgium
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Gent University, Karel Lodewijk Ledeganckstraat 35, 9000, Gent, Belgium
| | - Martijn Callens
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven- KU Leuven, Campus KULAK, E. Sabbelaan 53, 8500 Kortrijk, Belgium
- Animal Sciences Unit - Aquatic Environment and Quality, Flanders Research Institute for Agriculture, Fisheries and Food, Oostende 8400, Belgium
| | - Lore Bulteel
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven- KU Leuven, Campus KULAK, E. Sabbelaan 53, 8500 Kortrijk, Belgium
| | - Ellen Decaestecker
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven- KU Leuven, Campus KULAK, E. Sabbelaan 53, 8500 Kortrijk, Belgium
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6
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Carrillo MP, Sevilla M, Casado M, Piña B, Pastor López E, Matamoros V, Vila-Costa M, Barata C. Impact of the antibiotic doxycycline on the D. magna reproduction, associated microbiome and antibiotic resistance genes in treated wastewater conditions. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 334:122188. [PMID: 37442322 DOI: 10.1016/j.envpol.2023.122188] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/02/2023] [Accepted: 07/11/2023] [Indexed: 07/15/2023]
Abstract
Wastewater Treatment Plant (WWTP) effluents are important sources of antibiotics, antibiotic resistance genes (ARGs) and resistant bacteria that threaten aquatic biota and human heath. Antibiotic effects on host-associated microbiomes, spread of ARGs and the consequences for host health are still poorly described. This study investigated changes of the Daphnia magna associated microbiome exposed to the recalcitrant antibiotic doxycycline under artificial reconstituted lab water media (lab water) and treated wastewater media. D. magna individual juveniles were exposed for 10 days to treated wastewater with and without doxycycline, and similarly in lab water. We analysed 16 S rRNA gene sequences to assess changes in community structure, monitored Daphnia offspring production and quantified ARGs abundances by qPCR from both Daphnia and water (before and after the exposure). Results showed that doxycycline and media (lab water or wastewater) had a significant effect modulating Daphnia-associated microbiome composition and one of the most discriminant taxa was Enterococcus spp. Moreover, in lab water, doxycycline reduced the presence of Limnohabitans sp., which are dominant bacteria of the D. magna-associated microbiome and impaired Daphnia reproduction. Contrarily, treated wastewater increased diversity and richness of Daphnia-associated microbiome and promoted fecundity. In addition, the detected ARG genes in both lab water and treated wastewater medium included the qnrS1, sul1, and blaTEM, and the integron-related intI1 gene. The treated wastewater contained about 10 times more ARGs than lab water alone. Furthermore, there was an increase of sul1 in Daphnia cultured in treated wastewater compared to lab water. In addition, there were signs of a higher biodegradation of doxycycline by microbiomes of treated wastewater in comparison to lab water. Thus, results suggest that Daphnia-associated microbiomes are influenced by their environment, and that bacterial communities present in treated wastewater are better suited to cope with the effects of antibiotics.
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Affiliation(s)
- Maria Paula Carrillo
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Jordi Girona 18, 08034, Catalonia, Spain
| | - Marina Sevilla
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Jordi Girona 18, 08034, Catalonia, Spain
| | - Marta Casado
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Jordi Girona 18, 08034, Catalonia, Spain
| | - Benjamin Piña
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Jordi Girona 18, 08034, Catalonia, Spain
| | - Edward Pastor López
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Jordi Girona 18, 08034, Catalonia, Spain
| | - Victor Matamoros
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Jordi Girona 18, 08034, Catalonia, Spain
| | - Maria Vila-Costa
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Jordi Girona 18, 08034, Catalonia, Spain
| | - Carlos Barata
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Jordi Girona 18, 08034, Catalonia, Spain.
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7
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Li Z, Lu T, Li M, Mortimer M, Guo LH. Direct and gut microbiota-mediated toxicities of environmental antibiotics to fish and aquatic invertebrates. CHEMOSPHERE 2023; 329:138692. [PMID: 37059203 DOI: 10.1016/j.chemosphere.2023.138692] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
The accumulation of antibiotics in the environment has ecological impacts that have received less attention than the human health risks of antibiotics, although the effects could be far-reaching. This review discusses the effects of antibiotics on the health of fish and zooplankton, manifesting in direct or dysbiosis-mediated physiological impairment. Acute effects of antibiotics in these organism groups are usually induced at high concentrations (LC50 at ∼100-1000 mg/L) that are not commonly present in aquatic environments. However, when exposed to sub-lethal, environmentally relevant levels of antibiotics (ng/L-μg/L) disruption of physiological homeostasis, development, and fecundity can occur. Antibiotics at similar or lower concentrations can induce dysbiosis of gut microbiota which can affect the health of fish and invertebrates. We show that the data about molecular-level effects of antibiotics at low exposure concentrations are limited, hindering environmental risk assessment and species sensitivity analysis. Fish and crustaceans (Daphnia sp.) were the two groups of aquatic organisms used most often for antibiotic toxicity testing, including microbiota analysis. While low levels of antibiotics impact the composition and function of gut microbiota in aquatic organisms, the correlation and causality of these changes to host physiology are not straightforward. In some cases, negative or lack of correlation have occurred, and, unexpectedly, gut microbial diversity has been unaffected or increased upon exposure to environmental levels of antibiotics. Efforts to incorporate functional analyses of gut microbiota are beginning to provide valuable mechanistic information, but more data is needed for ecological risk assessment of antibiotics.
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Affiliation(s)
- Zhi Li
- College of Life Science, China Jiliang University, Hangzhou, Zhejiang, 310018, China; Institute of Environmental and Health Sciences, China Jiliang University, Hangzhou, Zhejiang, 310018, China
| | - Tingyu Lu
- College of Life Science, China Jiliang University, Hangzhou, Zhejiang, 310018, China; Institute of Environmental and Health Sciences, China Jiliang University, Hangzhou, Zhejiang, 310018, China
| | - Minjie Li
- Institute of Environmental and Health Sciences, China Jiliang University, Hangzhou, Zhejiang, 310018, China; College of Quality and Safety Engineering, China Jiliang University, Hangzhou, Zhejiang, 310018, China
| | - Monika Mortimer
- Institute of Environmental and Health Sciences, China Jiliang University, Hangzhou, Zhejiang, 310018, China; College of Quality and Safety Engineering, China Jiliang University, Hangzhou, Zhejiang, 310018, China.
| | - Liang-Hong Guo
- Institute of Environmental and Health Sciences, China Jiliang University, Hangzhou, Zhejiang, 310018, China; College of Quality and Safety Engineering, China Jiliang University, Hangzhou, Zhejiang, 310018, China.
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8
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Rajarajan A, Wolinska J, Walser JC, Dennis SR, Spaak P. Host-Associated Bacterial Communities Vary Between Daphnia galeata Genotypes but Not by Host Genetic Distance. MICROBIAL ECOLOGY 2023; 85:1578-1589. [PMID: 35486140 PMCID: PMC10167167 DOI: 10.1007/s00248-022-02011-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 04/08/2022] [Indexed: 05/10/2023]
Abstract
Host genotype may shape host-associated bacterial communities (commonly referred to as microbiomes). We sought to determine (a) whether bacterial communities vary among host genotypes in the water flea Daphnia galeata and (b) if this difference is driven by the genetic distance between host genotypes, by using D. galeata genotypes hatched from sediments of different time periods. We used 16S amplicon sequencing to profile the gut and body bacterial communities of eight D. galeata genotypes hatched from resting eggs; these were isolated from two distinct sediment layers (dating to 1989 and 2009) of a single sediment core of the lake Greifensee, and maintained in a common garden in laboratory cultures for 5 years. In general, bacterial community composition varied in both the Daphnia guts and bodies; but not between genotypes from different sediment layers. Specifically, genetic distances between host genotypes did not correlate with beta diversity of bacterial communities in Daphnia guts and bodies. Our results indicate that Daphnia bacterial community structure is to some extent determined by a host genetic component, but that genetic distances between hosts do not correlate with diverging bacterial communities.
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Affiliation(s)
- Amruta Rajarajan
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland.
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Institut Für Biologie, Freie Universität Berlin (FU), Berlin, Germany
| | | | - Stuart R Dennis
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Piet Spaak
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
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9
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Jordán F. The network perspective: Vertical connections linking organizational levels. Ecol Modell 2022. [DOI: 10.1016/j.ecolmodel.2022.110112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Papp M, Békési L, Farkas R, Makrai L, Judge MF, Maróti G, Tőzsér D, Solymosi N. Natural diversity of the honey bee (Apis mellifera) gut bacteriome in various climatic and seasonal states. PLoS One 2022; 17:e0273844. [PMID: 36083885 PMCID: PMC9462563 DOI: 10.1371/journal.pone.0273844] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
As pollinators and producers of numerous human-consumed products, honey bees have great ecological, economic and health importance. The composition of their bacteriota, for which the available knowledge is limited, is essential for their body's functioning. Based on our survey, we performed a metagenomic analysis of samples collected by repeated sampling. We used geolocations that represent the climatic types of the study area over two nutritionally extreme periods (March and May) of the collection season. Regarding bacteriome composition, a significant difference was found between the samples from March and May. The samples' bacteriome from March showed a significant composition difference between cooler and warmer regions. However, there were no significant bacteriome composition differences among the climatic classes of samples taken in May. Based on our results, one may conclude that the composition of healthy core bacteriomes in honey bees varies depending on the climatic and seasonal conditions. This is likely due to climatic factors and vegetation states determining the availability and nutrient content of flowering plants. The results of our study prove that in order to gain a thorough understanding of a microbiome's natural diversity, we need to obtain the necessary information from extreme ranges within the host's healthy state.
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Affiliation(s)
- Márton Papp
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | - László Békési
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
| | - Róbert Farkas
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
| | - László Makrai
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Budapest, Hungary
| | - Maura Fiona Judge
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | - Gergely Maróti
- Plant Biology Institute of the Biological Research Center, Szeged, Hungary
- Faculty of Water Sciences, University of Public Service, Baja, Hungary
| | - Dóra Tőzsér
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | - Norbert Solymosi
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
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11
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Rajarajan A, Wolinska J, Walser JC, Mäder M, Spaak P. Infection by a eukaryotic gut parasite in wild Daphnia sp. associates with a distinct bacterial community. FEMS Microbiol Ecol 2022; 98:6677393. [PMID: 36026529 PMCID: PMC9869925 DOI: 10.1093/femsec/fiac097] [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: 04/01/2022] [Revised: 07/04/2022] [Accepted: 08/23/2022] [Indexed: 01/26/2023] Open
Abstract
Host-associated bacterial communities play an important role in host fitness and resistance to diseases. Yet, few studies have investigated tripartite interaction between a host, parasite and host-associated bacterial communities in natural settings. Here, we use 16S rRNA gene amplicon sequencing to compare gut- and body- bacterial communities of wild water fleas belonging to the Daphnia longispina complex, between uninfected hosts and those infected with the common and virulent eukaryotic gut parasite Caullerya mesnili (Family: Ichthyosporea). We report community-level changes in host-associated bacteria with the presence of the parasite infection; namely decreased alpha diversity and increased beta diversity at the site of infection, i.e. host gut (but not host body). We also report decreased abundance of bacterial taxa proposed elsewhere to be beneficial for the host, and an appearance of taxa specifically associated with infected hosts. Our study highlights the host-microbiota-infection link in a natural system and raises questions about the role of host-associated microbiota in natural disease epidemics as well as the functional roles of bacteria specifically associated with infected hosts.
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Affiliation(s)
- Amruta Rajarajan
- Corresponding author: Office BU-G09, Überlandstrasse 133, 8600 Dübendorf, Zürich, Switzerland. E-mail: and
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany,Department of Biology, Chemistry, Pharmacy, Institut für Biologie, Freie Universität Berlin (FU), 14195 Berlin, Germany
| | - Jean-Claude Walser
- Department of Environmental systems science (D-USYS), Genetic Diversity Centre (GDC), Federal Institute of Technology (ETH) Zürich, 8092, Zürich, Switzerland
| | - Minea Mäder
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Zürich, Switzerland
| | - Piet Spaak
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Zürich, Switzerland
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12
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Akbar S, Gu L, Sun Y, Zhang L, Lyu K, Huang Y, Yang Z. Understanding host-microbiome-environment interactions: Insights from Daphnia as a model organism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:152093. [PMID: 34863741 DOI: 10.1016/j.scitotenv.2021.152093] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/21/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
Microbes perform a variety of vital functions that are essential for healthy ecosystems, ranging from nutrient recycling, antibiotic production and waste decomposition. In many animals, microbes become an integral part by establishing diverse communities collectively termed as "microbiome/s". Microbiomes defend their hosts against pathogens and provide essential nutrients necessary for their growth and reproduction. The microbiome is a polygenic trait that is dependent on host genotype and environmental variables. However, the alteration of microbiomes by stressful condition and their recovery is still poorly understood. Despite rapid growth in host-associated microbiome studies, very little is known about how they can shape ecological processes. Here, we review current knowledge on the microbiome of Daphnia, its role in fitness, alteration by different stressors, and the ecological and evolutionary aspects of host microbiome interactions. We further discuss how variation in Daphnia physiology, life history traits, and microbiome interactive responses to biotic and abiotic factors could impact patterns of microbial diversity in the total environment, which drives ecosystem function in many freshwater environments. Our literature review provides evidence that microbiome is essential for Daphnia growth, reproduction and tolerance against stressors. Though the core and flexible microbiome of Daphnia is still debatable, it is clear that the Daphnia microbiome is highly dependent on interactions among host genotype, diet and the environment. Different environmental factors alter the microbiome composition and diversity of Daphnia and reduce their fitness. These interactions could have important implications in shaping microbial patterns and their recycling as Daphnia are keystone species in freshwater ecosystem. This review provides a framework for studying these complex relationships to gain a better understanding of the ecological and evolutionary roles of the microbiome.
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Affiliation(s)
- Siddiq Akbar
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Lei Gu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Yunfei Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Lu Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Kai Lyu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Yuan Huang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Zhou Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China.
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