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Nguyen TD, Itayama T, Tran QV, Dao TS, Iqbal MS, Pham TL. Ecotoxicity of the fluoroquinolone antibiotic delafloxacin to the water flea Simocephalus vetulus and its offspring under the influence of calcium modulation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171450. [PMID: 38438028 DOI: 10.1016/j.scitotenv.2024.171450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/21/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Delafloxacin (DFX), one of the latest additions to the fluoroquinolone antibiotics, is gaining heightened recognition in human therapy due to its potential antibacterial efficacy in a wide range of applications. Concerns have arisen regarding its presence in the environment and its potential interactions with multivalent metals, such as calcium (Ca). The present study investigated the trans- and multigenerational effects of environmentally projected concentrations of DFX (100-400 μg DFX L-1) on individual- and population-level responses of parental S. vetulus (F0) and its descendants (F1) under normal (26 mg L-1) and high (78 mg L-1) Ca conditions. Exposure of the F0 generation to DFX under the normal Ca condition resulted in reduced juvenile body length (JBL), increased age-specific survival rate (lx), indicating prolonged developmental time, reduced age-specific fecundity rate (mx), and decreased population growth rate (rm). Under the high Ca condition, JBL, mx, and rm were adversely affected. Transgenerational effects of DFX existed, as F1 individuals exhibited persistent suppressions in at least one endpoint under both Ca conditions even after being transferred to a clear medium. Continuous exposure of the F1 generation to DFX had negative impacts on JBL, mx, and rm under the normal Ca condition, and on JBL and rm under the high Ca condition. However, cumulative effects were not observed, suggesting the potential development of tolerance to DFX in the F1 organisms. These findings suggest that DFX is a harmful compound for the non-target model organism S. vetulus and reveal a potential antagonism between DFX and Ca. Nevertheless, the interaction between other (fluoro)quinolones and Ca remains unclear, necessitating further research to establish this phenomenon more comprehensively, including understanding the interaction mechanism in ecotoxicological contexts.
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Affiliation(s)
- Tan-Duc Nguyen
- Department of Science and Technology, Nagasaki University, Nagasaki City, Japan; Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Protection, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China.
| | - Tomoaki Itayama
- Department of Science and Technology, Nagasaki University, Nagasaki City, Japan
| | - Quang Vinh Tran
- Asian Centre for Water Research (CARE), Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City, Viet Nam
| | - Thanh-Son Dao
- Faculty of Environment and Natural Resources, Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City, Viet Nam; Vietnam National University Ho Chi Minh City, Ho Chi Minh City, Viet Nam
| | | | - Thanh Luu Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology (VAST), Hanoi City, Viet Nam; Institute of Tropical Biology, Vietnam Academy of Science and Technology (VAST), Ho Chi Minh City, Viet Nam
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2
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Chaturvedi A, Li X, Dhandapani V, Marshall H, Kissane S, Cuenca-Cambronero M, Asole G, Calvet F, Ruiz-Romero M, Marangio P, Guigó R, Rago D, Mirbahai L, Eastwood N, Colbourne J, Zhou J, Mallon E, Orsini L. The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome. Nucleic Acids Res 2023; 51:9785-9803. [PMID: 37638757 PMCID: PMC10570034 DOI: 10.1093/nar/gkad685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023] Open
Abstract
Properties that make organisms ideal laboratory models in developmental and medical research are often the ones that also make them less representative of wild relatives. The waterflea Daphnia magna is an exception, by both sharing many properties with established laboratory models and being a keystone species, a sentinel species for assessing water quality, an indicator of environmental change and an established ecotoxicology model. Yet, Daphnia's full potential has not been fully exploited because of the challenges associated with assembling and annotating its gene-rich genome. Here, we present the first hologenome of Daphnia magna, consisting of a chromosomal-level assembly of the D. magna genome and the draft assembly of its metagenome. By sequencing and mapping transcriptomes from exposures to environmental conditions and from developmental morphological landmarks, we expand the previously annotates gene set for this species. We also provide evidence for the potential role of gene-body DNA-methylation as a mutagen mediating genome evolution. For the first time, our study shows that the gut microbes provide resistance to commonly used antibiotics and virulence factors, potentially mediating Daphnia's environmental-driven rapid evolution. Key findings in this study improve our understanding of the contribution of DNA methylation and gut microbiota to genome evolution in response to rapidly changing environments.
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Affiliation(s)
- Anurag Chaturvedi
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Xiaojing Li
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Vignesh Dhandapani
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Hollie Marshall
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
- Department of Genetics and Genome Biology, the University of Leicester, Leicester LE1 7RH, UK
| | - Stephen Kissane
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Maria Cuenca-Cambronero
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
- Aquatic Ecology Group, University of Vic - Central University of Catalonia, 08500 Vic, Spain
| | - Giovanni Asole
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Ferriol Calvet
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Marina Ruiz-Romero
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Paolo Marangio
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Daria Rago
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Leda Mirbahai
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Niamh Eastwood
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - John K Colbourne
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Jiarui Zhou
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Eamonn Mallon
- Department of Genetics and Genome Biology, the University of Leicester, Leicester LE1 7RH, UK
| | - Luisa Orsini
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
- The Alan Turing Institute, British Library, London NW1 2DB, UK
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3
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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: 0] [Impact Index Per Article: 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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4
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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: 6] [Impact Index Per Article: 6.0] [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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5
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Brown JJ, Jandová A, Jeffs CT, Higgie M, Nováková E, Lewis OT, Hrček J. Microbiome Structure of a Wild Drosophila Community along Tropical Elevational Gradients and Comparison to Laboratory Lines. Appl Environ Microbiol 2023; 89:e0009923. [PMID: 37154737 DOI: 10.1128/aem.00099-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Variation along environmental gradients in host-associated microbial communities is not well understood compared to free-living microbial communities. Because elevational gradients may serve as natural proxies for climate change, understanding patterns along these gradients can inform our understanding of the threats hosts and their symbiotic microbes face in a warming world. In this study, we analyzed bacterial microbiomes from pupae and adults of four Drosophila species native to Australian tropical rainforests. We sampled wild individuals at high and low elevations along two mountain gradients to determine natural diversity patterns. Further, we sampled laboratory-reared individuals from isofemale lines established from the same localities to see if any natural patterns are retained in the lab. In both environments, we controlled for diet to help elucidate other deterministic patterns of microbiome composition. We found small but significant differences in Drosophila bacterial community composition across elevation, with some notable taxonomic differences between different Drosophila species and sites. Further, we found that field-collected fly pupae had significantly richer microbiomes than laboratory-reared pupae. We also found similar microbiome composition in both types of provided diet, suggesting that the significant differences found among Drosophila microbiomes are the products of surrounding environments with different bacterial species pools, possibly bound to elevational differences in temperature. Our results suggest that comparative studies between lab and field specimens help reveal the true variability in microbiome communities that can exist within a single species. IMPORTANCE Bacteria form microbial communities inside most higher-level organisms, but we know little about how the microbiome varies along environmental gradients and between natural host populations and laboratory colonies. To explore such effects on insect-associated microbiomes, we studied the gut microbiome in four Drosophila species over two mountain gradients in tropical Australia. We also compared these data to individuals kept in the laboratory to understand how different settings changed microbiome communities. We found that field-sampled individuals had significantly higher microbiome diversity than those from the lab. In wild Drosophila populations, elevation explains a small but significant amount of the variation in their microbial communities. Our study highlights the importance of environmental bacterial sources for Drosophila microbiome composition across elevational gradients and shows how comparative studies help reveal the true flexibility in microbiome communities that can exist within a species.
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Affiliation(s)
- Joel J Brown
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Anna Jandová
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | | | - Megan Higgie
- College of Science & Engineering, James Cook University, Townsville, Queensland, Australia
| | - Eva Nováková
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Owen T Lewis
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Jan Hrček
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
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6
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Akbar S, Li X, Ding Z, Liu Q, Huang J, Zhou Q, Gu L, Yang Z. Disentangling Diet- and Medium-Associated Microbes in Shaping Daphnia Gut Microbiome. MICROBIAL ECOLOGY 2022; 84:911-921. [PMID: 34714368 DOI: 10.1007/s00248-021-01900-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 10/11/2021] [Indexed: 05/09/2023]
Abstract
Host genotype and environment are considered crucial factors in shaping Daphnia gut microbiome composition. Among the environmental factors, diet is an important factor that regulates Daphnia microbiome. Most of the studies only focused on the use of axenic diet and non-sterile medium to investigate their effects on Daphnia microbiome. However, in natural environment, Daphnia diets such as phytoplankton are associated with microbes and could affect Daphnia microbiome composition and fitness, but remain relatively poorly understood compared to that of axenic diet. To test this, we cultured two Daphnia magna genotypes (genotype-1 and genotype-2) in sterile medium and fed with axenic diet. To check the effects of algal diet-associated microbes versus free water-related microbes, Daphnia were respectively inoculated with three different inoculums: medium microbial inoculum, diet-associated microbial inoculum, and medium and diet-mixed microbial inoculum. Daphnia were cultured for 3 weeks and their gut microbiome and life history traits were recorded. Results showed that Daphnia inoculated with medium microbial inoculum were dominated by Comamonadaceae in both genotypes. In Daphnia inoculated with mixed inoculum, genotype-1 microbiome was highly changed, whereas genotype-2 microbiome was slightly altered. Daphnia inoculated with diet microbial inoculum has almost the same microbiome in both genotypes. The total number of neonates and body size were significantly reduced in Daphnia inoculated with diet microbial inoculum regardless of genotype compared to all other treatments. Overall, this study shows that the microbiome of Daphnia is flexible and varies with genotype and diet- and medium-associated microbes, but not every bacteria is beneficial to Daphnia, and only symbionts can increase Daphnia performance.
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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
| | - Xianxian Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Zihao Ding
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Qi Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Jing Huang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Qiming Zhou
- 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
| | - 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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7
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Cooper RO, Tjards S, Rischling J, Nguyen DT, Cressler CE. Multiple generations of antibiotic exposure and isolation influence host fitness and the microbiome in a model zooplankton species. FEMS Microbiol Ecol 2022; 98:6648098. [PMID: 35862853 DOI: 10.1093/femsec/fiac082] [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: 01/24/2022] [Revised: 07/04/2022] [Accepted: 08/09/2022] [Indexed: 11/14/2022] Open
Abstract
Chronic antibiotic exposure impacts host health through changes to the microbiome. The detrimental effects of antibiotic perturbation on microbiome structure and function after one host generation of exposure have been well-studied, but less is understood about multigenerational effects of antibiotic exposure and subsequent recovery. In this study, we examined microbiome composition and host fitness across five generations of exposure to antibiotics in the model zooplankton host Daphnia magna. By utilizing a split-brood design where half of the offspring from antibiotic-exposed parents were allowed to recover and half were maintained in antibiotics, we examined recovery and resilience of the microbiome. Unexpectedly, we discovered that isolation of single host individuals across generations exerted a strong effect on microbiome composition, with microbiome diversity decreasing over generations regardless of treatment while host body size and cumulative reproduction increased across generations. Though antibiotics did cause substantial changes to microbiome composition within a generation, recovery generally occurred in one generation regardless of the number of prior generations spent in antibiotics. Our results demonstrate that isolation of individual hosts leads to stochastic extinction of less abundant taxa in the microbiome, suggesting that these taxa are likely maintained via transmission in host populations.
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Affiliation(s)
- Reilly O Cooper
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Sarah Tjards
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jessica Rischling
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - David T Nguyen
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Clayton E Cressler
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
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8
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Alberdi A, Andersen SB, Limborg MT, Dunn RR, Gilbert MTP. Disentangling host-microbiota complexity through hologenomics. Nat Rev Genet 2022; 23:281-297. [PMID: 34675394 DOI: 10.1038/s41576-021-00421-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 02/07/2023]
Abstract
Research on animal-microbiota interactions has become a central topic in biological sciences because of its relevance to basic eco-evolutionary processes and applied questions in agriculture and health. However, animal hosts and their associated microbial communities are still seldom studied in a systemic fashion. Hologenomics, the integrated study of the genetic features of a eukaryotic host alongside that of its associated microbes, is becoming a feasible - yet still underexploited - approach that overcomes this limitation. Acknowledging the biological and genetic properties of both hosts and microbes, along with the advantages and disadvantages of implemented techniques, is essential for designing optimal studies that enable some of the major questions in biology to be addressed.
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Affiliation(s)
- Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Sandra B Andersen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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9
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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: 8] [Impact Index Per Article: 4.0] [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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Nguyen TD, Itayama T, Ramaraj R, Iwami N, Shimizu K, Dao TS, Pham TL, Maseda H. Chronic ecotoxicology and statistical investigation of ciprofloxacin and ofloxacin to Daphnia magna under extendedly long-term exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 291:118095. [PMID: 34537598 DOI: 10.1016/j.envpol.2021.118095] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/09/2021] [Accepted: 08/31/2021] [Indexed: 05/22/2023]
Abstract
Ciprofloxacin (CFX) and ofloxacin (OFX) are two of the most often used fluoroquinolone antibiotics, and their residues are found in large amounts in various aquatic settings. However, the toxicity tests of CFX using eukaryotic organisms such as Daphnia magna are inadequate, and the test result of OFX is currently unknown. Therefore, the chronic toxicity test for D. magna was performed during 42 days under exposure to CFX and OFX concentrations of 50, 500, and 5000 μg L-1. All exposure conditions did not cause mortality for D. magna. CFX exposure at 500 μg L-1 resulted in an earlier oogenesis date and increased brood size in the second birth. The Poisson-based generalized linear mixed-effects model revealed that the reduction of fertility was statistically significant for the CFX and OFX exposures at 5000 μg L-1. On the other hand, the production of dead eggs as offspring degradation was also found significantly as maternal D. magna exposed to antibiotics at 5000 μg L-1. In addition, following long-term exposure to antibiotics, maternal adaptation to antibiotics was established for offspring deterioration and fertility. However, the OFX exposure showed that the fertility-suppressed effects continued for a longer period than the CFX exposure. Although no rational explanation has yet been given for the more substantial effect of OFX on reducing fertility than CFX, molecular cell biology and symbiotic microbial flora derived from previous studies could explain our ecotoxicological results. This study is the first report for the OFX chronic toxicities on D. magna by comparing it to the toxicity of CFX. Our study contributes to guiding the future impact assessment of fluoroquinolone antibiotic pollution on ecosystems, including the need for new statistical methods in ecotoxicological studies.
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Affiliation(s)
- Tan-Duc Nguyen
- Graduate School of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki-shi, Japan
| | - Tomoaki Itayama
- Graduate School of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki-shi, Japan.
| | - Rameshprabu Ramaraj
- School of Renewable Energy, Maejo University, Sansai, Chiang Mai, 50290, Thailand
| | - Norio Iwami
- School of Science and Engineering, Meise University, 2-1-1 Hodokubo, Hino-shi, Tokyo, 191-8506, Japan
| | - Kazuya Shimizu
- Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba-shi, Ibaraki, Japan
| | - Thanh-Son Dao
- Faculty of Environment and Natural Resources, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Viet Nam; Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam
| | - Thanh-Luu Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet Street, Cau Giay District, Hanoi, 100000, Viet Nam; Institute of Tropical Biology, Vietnam Academy of Science and Technology (VAST), 85 Tran Quoc Toan Street, District 3, Ho Chi Minh City, 700000, Viet Nam
| | - Hideaki Maseda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka, 563-8577, Japan
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