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Ma C, Xu C, Zhang T, Mu Q, Lv J, Xing Q, Yang Z, Xu Z, Guan Y, Chen C, Ni K, Dai X, Ding W, Hu J, Bao Z, Wang S, Liu P. Tracking the hologenome dynamics in aquatic invertebrates by the holo-2bRAD approach. Commun Biol 2024; 7:827. [PMID: 38972908 PMCID: PMC11228047 DOI: 10.1038/s42003-024-06509-7] [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: 12/21/2023] [Accepted: 06/26/2024] [Indexed: 07/09/2024] Open
Abstract
The "hologenome" concept is an increasingly popular way of thinking about microbiome-host for marine organisms. However, it is challenging to track hologenome dynamics because of the large amount of material, with tracking itself usually resulting in damage or death of the research object. Here we show the simple and efficient holo-2bRAD approach for the tracking of hologenome dynamics in marine invertebrates (i.e., scallop and shrimp) from one holo-2bRAD library. The stable performance of our approach was shown with high genotyping accuracy of 99.91% and a high correlation of r > 0.99 for the species-level profiling of microorganisms. To explore the host-microbe association underlying mass mortality events of bivalve larvae, core microbial species changed with the stages were found, and two potentially associated host SNPs were identified. Overall, our research provides a powerful tool with various advantages (e.g., cost-effective, simple, and applicable for challenging samples) in genetic, ecological, and evolutionary studies.
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Affiliation(s)
- Cen Ma
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, China
| | - Chang Xu
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Tianqi Zhang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qianqian Mu
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Jia Lv
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Qiang Xing
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, China
| | - Zhihui Yang
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Zhenyuan Xu
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Yalin Guan
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chengqin Chen
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Kuo Ni
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Dai
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Institute of Gerontology, Geriatrics Center, University of Michigan, Ann Arbor, MI, USA
| | - Wei Ding
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jingjie Hu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Zhenmin Bao
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Shi Wang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Pingping Liu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
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Horváthová T, Lafuente E, Bartels J, Wallisch J, Vorburger C. Tolerance to environmental pollution in the freshwater crustacean Asellus aquaticus: A role for the microbiome. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13252. [PMID: 38783543 PMCID: PMC11116767 DOI: 10.1111/1758-2229.13252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/13/2024] [Indexed: 05/25/2024]
Abstract
Freshwater habitats are frequently contaminated by diverse chemicals of anthropogenic origin, collectively referred to as micropollutants, that can have detrimental effects on aquatic life. The animals' tolerance to micropollutants may be mediated by their microbiome. If polluted aquatic environments select for contaminant-degrading microbes, the acquisition of such microbes by the host may increase its tolerance to pollution. Here we tested for the potential effects of the host microbiome on the growth and survival of juvenile Asellus aquaticus, a widespread freshwater crustacean. Using faecal microbiome transplants, we provided newly hatched juveniles with the microbiome isolated from donor adults reared in either clean or micropollutant-contaminated water and, after transplantation, recipient juveniles were reared in water with and without micropollutants. The experiment revealed a significant negative effect of the micropollutants on the survival of juvenile isopods regardless of the received faecal microbiome. The micropollutants had altered the composition of the bacterial component of the donors' microbiome, which in turn influenced the microbiome of juvenile recipients. Hence, we show that relatively high environmental concentrations of micropollutants reduce survival and alter the microbiome composition of juvenile A. aquaticus, but we have no evidence that tolerance to micropollutants is modulated by their microbiome.
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Affiliation(s)
- Terézia Horváthová
- Department of Aquatic EcologyEawagDübendorfSwitzerland
- Institute of Soil Biology and BiochemistryBiology Centre CASČeské BudějoviceCzechia
| | - Elvira Lafuente
- Department of Aquatic EcologyEawagDübendorfSwitzerland
- Instituto Gulbenkian de CiênciaOeirasPortugal
| | | | | | - Christoph Vorburger
- Department of Aquatic EcologyEawagDübendorfSwitzerland
- D‐USYS, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
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Liu F, Ryu T, Ravasi T, Wang X, Wang G, Li Z. Niche-dependent sponge hologenome expression profiles and the host-microbes interplay: a case of the hawaiian demosponge Mycale Grandis. ENVIRONMENTAL MICROBIOME 2024; 19:22. [PMID: 38589941 PMCID: PMC11000336 DOI: 10.1186/s40793-024-00563-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/14/2024] [Indexed: 04/10/2024]
Abstract
BACKGROUND Most researches on sponge holobionts focus primarily on symbiotic microbes, yet data at the level of the sponge hologenome are still relatively scarce. Understanding of the sponge host and its microbial gene expression profiles and the host-microbes interplay in different niches represents a key aspect of sponge hologenome. Using the Hawaiian demosponge Mycale grandis in different niches as a model, i.e. on rocks, on the surface of coral Porites compressa, under alga Gracilaria salicornia, we compared the bacterial and fungal community structure, functional gene diversity, expression pattern and the host transcriptome by integrating open-format (deep sequencing) and closed-format (GeoChip microarray) high-throughput techniques. RESULTS Little inter-niche variation in bacterial and fungal phylogenetic diversity was detected for M. grandis in different niches, but a clear niche-dependent variability in the functional gene diversity and expression pattern of M. grandis host and its symbiotic microbiota was uncovered by GeoChip microarray and transcriptome analyses. Particularly, sponge host genes related to innate immunity and microbial recognition showed a strong correlation with the microbial symbionts' functional gene diversity and transcriptional richness in different niches. The cross-niche variability with respect to the symbiont functional gene diversity and the transcriptional richness of M. grandis holobiont putatively reflects the interplay of niche-specific selective pressure and the symbiont functional diversity. CONCLUSIONS Niche-dependent gene expression profiles of M. grandis hologenome and the host-microbes interplay were suggested though little inter-niche variation in bacterial and fungal diversity was detected, particularly the sponge innate immunity was found to be closely related to the symbiotic microbes. Altogether, these findings provide novel insights into the black box of one sponge holobiont in different niches at the hologenome level.
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Affiliation(s)
- Fang Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China
| | - Taewoo Ryu
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, 904-0495, Okinawa, Japan
| | - Timothy Ravasi
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, 904-0495, Okinawa, Japan
| | - Xin Wang
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 32611, Gainesville, FL, USA
| | - Guangyi Wang
- School of Environmental Science and Engineering, Tianjin University, 300072, Tianjin, P. R. China
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China.
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, 200240, Shanghai, P. R. China.
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Pearman WS, Duffy GA, Liu XP, Gemmell NJ, Morales SE, Fraser CI. Macroalgal microbiome biogeography is shaped by environmental drivers rather than geographical distance. ANNALS OF BOTANY 2024; 133:169-182. [PMID: 37804485 PMCID: PMC10921836 DOI: 10.1093/aob/mcad151] [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: 07/06/2023] [Accepted: 10/06/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND AND AIMS Contrasting patterns of host and microbiome biogeography can provide insight into the drivers of microbial community assembly. Distance-decay relationships are a classic biogeographical pattern shaped by interactions between selective and non-selective processes. Joint biogeography of microbiomes and their hosts is of increasing interest owing to the potential for microbiome-facilitated adaptation. METHODS In this study, we examine the coupled biogeography of the model macroalga Durvillaea and its microbiome using a combination of genotyping by sequencing (host) and 16S rRNA amplicon sequencing (microbiome). Alongside these approaches, we use environmental data to characterize the relationship between the microbiome, the host, and the environment. KEY RESULTS We show that although the host and microbiome exhibit shared biogeographical structure, these arise from different processes, with host biogeography showing classic signs of geographical distance decay, but with the microbiome showing environmental distance decay. Examination of microbial subcommunities, defined by abundance, revealed that the abundance of microbes is linked to environmental selection. As microbes become less common, the dominant ecological processes shift away from selective processes and towards neutral processes. Contrary to expectations, we found that ecological drift does not promote structuring of the microbiome. CONCLUSIONS Our results suggest that although host macroalgae exhibit a relatively 'typical' biogeographical pattern of declining similarity with increasing geographical distance, the microbiome is more variable and is shaped primarily by environmental conditions. Our findings suggest that the Baas Becking hypothesis of 'everything is everywhere, the environment selects' might be a useful hypothesis to understand the biogeography of macroalgal microbiomes. As environmental conditions change in response to anthropogenic influences, the processes structuring the microbiome of macroalgae might shift, whereas those governing the host biogeography are less likely to change. As a result, increasingly decoupled host-microbe biogeography might be observed in response to such human influences.
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Affiliation(s)
- William S Pearman
- Department of Marine Science, University of Otago, New Zealand
- Department of Anatomy, School of Biomedical Sciences, University of Otago, New Zealand
- Department of Microbiology & Immunology, School of Biomedical Sciences, University of Otago, New Zealand
| | - Grant A Duffy
- Department of Marine Science, University of Otago, New Zealand
| | - Xiaoyue P Liu
- Department of Marine Science, University of Otago, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, New Zealand
| | - Sergio E Morales
- Department of Microbiology & Immunology, School of Biomedical Sciences, University of Otago, New Zealand
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Daniels BN, Nurge J, De Smet C, Sleeper O, White C, Davidson JM, Fidopiastis P. Microbiome composition and function within the Kellet's whelk perivitelline fluid. Microbiol Spectr 2024; 12:e0351423. [PMID: 38334378 PMCID: PMC10913743 DOI: 10.1128/spectrum.03514-23] [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: 10/02/2023] [Accepted: 01/17/2024] [Indexed: 02/10/2024] Open
Abstract
Microbiomes have gained significant attention in ecological research, owing to their diverse interactions and essential roles within different organismal ecosystems. Microorganisms, such as bacteria, archaea, and viruses, have profound impact on host health, influencing digestion, metabolism, immune function, tissue development, and behavior. This study investigates the microbiome diversity and function of Kellet's whelk (Kelletia kelletii) perivitelline fluid (PVF), which sustains thousands of developing K. kelletii embryos within a polysaccharide and protein matrix. Our core microbiome analysis reveals a diverse range of bacteria, with the Roseobacter genus being the most abundant. Additionally, genes related to host-microbe interactions, symbiosis, and quorum sensing were detected, indicating a potential symbiotic relationship between the microbiome and Kellet's whelk embryos. Furthermore, the microbiome exhibits gene expression related to antibiotic biosynthesis, suggesting a defensive role against pathogenic bacteria and potential discovery of novel antibiotics. Overall, this study sheds light on the microbiome's role in Kellet's whelk development, emphasizing the significance of host-microbe interactions in vulnerable life history stages. To our knowledge, ours is the first study to use 16S sequencing coupled with RNA sequencing (RNA-seq) to profile the microbiome of an invertebrate PVF.IMPORTANCEThis study provides novel insight to an encapsulated system with strong evidence of symbiosis between the microbial inhabitants and developing host embryos. The Kellet's whelk perivitelline fluid (PVF) contains microbial organisms of interest that may be providing symbiotic functions and potential antimicrobial properties during this vulnerable life history stage. This study, the first to utilize a comprehensive approach to investigating Kellet's whelk PVF microbiome, couples 16S rRNA gene long-read sequencing with RNA-seq. This research contributes to and expands our knowledge on the roles of beneficial host-associated microbes.
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Affiliation(s)
- Benjamin N. Daniels
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Jenna Nurge
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Chanel De Smet
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Olivia Sleeper
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Crow White
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Jean M. Davidson
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Pat Fidopiastis
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California, USA
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Díez-Vives C, Riesgo A. High compositional and functional similarity in the microbiome of deep-sea sponges. THE ISME JOURNAL 2024; 18:wrad030. [PMID: 38365260 PMCID: PMC10837836 DOI: 10.1093/ismejo/wrad030] [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: 11/30/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 02/18/2024]
Abstract
Sponges largely depend on their symbiotic microbes for their nutrition, health, and survival. This is especially true in high microbial abundance (HMA) sponges, where filtration is usually deprecated in favor of a larger association with prokaryotic symbionts. Sponge-microbiome association is substantially less understood for deep-sea sponges than for shallow water species. This is most unfortunate, since HMA sponges can form massive sponge grounds in the deep sea, where they dominate the ecosystems, driving their biogeochemical cycles. Here, we assess the microbial transcriptional profile of three different deep-sea HMA sponges in four locations of the Cantabrian Sea and compared them to shallow water HMA and LMA (low microbial abundance) sponge species. Our results reveal that the sponge microbiome has converged in a fundamental metabolic role for deep-sea sponges, independent of taxonomic relationships or geographic location, which is shared in broad terms with shallow HMA species. We also observed a large number of redundant microbial members performing the same functions, likely providing stability to the sponge inner ecosystem. A comparison between the community composition of our deep-sea sponges and another 39 species of HMA sponges from deep-sea and shallow habitats, belonging to the same taxonomic orders, suggested strong homogeneity in microbial composition (i.e. weak species-specificity) in deep sea species, which contrasts with that observed in shallow water counterparts. This convergence in microbiome composition and functionality underscores the adaptation to an extremely restrictive environment with the aim of exploiting the available resources.
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Affiliation(s)
- Cristina Díez-Vives
- Department of Systems Biology, Centro Nacional de Biotecnología, c/ Darwin, 3, 28049 Madrid, Spain
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
| | - Ana Riesgo
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), c/José Gutiérrez Abascal 2, 28006 Madrid, Spain
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Pratt CJ, Meili CH, Youssef NH, Hoback WW. Culture-independent analyses of carrion beetle (Coleoptera: Silphidae) secretion bacterial communities. Microbiol Spectr 2023; 11:e0169423. [PMID: 37874151 PMCID: PMC10714842 DOI: 10.1128/spectrum.01694-23] [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: 04/22/2023] [Accepted: 08/14/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE The manuscript explores the secretion bacterial community of carrion and burying beetles of the central plains of North America. A core secretion microbiome of 11 genera is identified. The host subfamily, secretion type, and collection locality significantly affects the secretion microbiome. Future culture-dependent studies from silphid secretions may identify novel antimicrobials and nontoxic compounds that can act as meat preservatives or sources for antimicrobials.
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Affiliation(s)
- Carrie J. Pratt
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Casey H. Meili
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - W. Wyatt Hoback
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma, USA
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Lv H, Li X, He D, Chen X, Liu M, Lan Y, Zhao J, Wang H, Yan Z. Genotype-Controlled Vertical Transmission Exerts Selective Pressure on Community Assembly of Salvia miltiorrhiza. MICROBIAL ECOLOGY 2023; 86:2934-2948. [PMID: 37667132 DOI: 10.1007/s00248-023-02295-7] [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: 05/07/2023] [Accepted: 08/27/2023] [Indexed: 09/06/2023]
Abstract
The plant's endophytic fungi play an important role in promoting host development and metabolism. Studies have shown that the factors affecting the assembly of the endophyte community mainly include host genotype, vertical transmission, and soil origin. However, we do not know the role of vertically transmitted endohytic fungi influences on the host-plant's endophytic community assembly. Salvia miltiorrhiza from three production areas were used as research objects; we constructed three production area genotypes of S. miltiorrhiza regenerated seedlings simultaneously. Based on high-throughput sequencing, we analyzed the effects of genotype, soil origin, and vertical transmission on endophytic fungal communities. The results show that the community of soil origins significantly affected the endophytic fungal community in the regenerated seedlings of S. miltiorrhiza. The influence of genotype on community composition occurs through a specific mechanism. Genotype may selectively screen certain communities into the seed, thereby exerting selection pressure on the community composition process of offspring. As the number of offspring increases gradually, the microbiota, controlled by genotype and transmitted vertically, stabilizes, ultimately resulting in a significant effect of genotype on community composition.Furthermore, we observed that the taxa influencing the active ingredients are also selected as the vertically transmitted community. Moreover, the absence of an initial vertically transmitted community in S. miltiorrhiza makes it more vulnerable to infection by pathogenic fungi. Therefore, it is crucial to investigate and comprehend the selection model of the vertically transmitted community under varying genotypes and soil conditions. This research holds significant implications for enhancing the quality and yield of medicinal plants and economic crops.
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Affiliation(s)
- Hongyang Lv
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaoyu Li
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dongmei He
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xin Chen
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Min Liu
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yin Lan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China
- Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jin Zhao
- State Key Laboratory of Quality Research in Chinese Medicine, Chengdu, China.
- Institute of Chinese Medical Sciences, University of Macau, Taipa, China.
| | - Hai Wang
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China.
- Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Zhuyun Yan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu, China.
- Chengdu University of Traditional Chinese Medicine, Chengdu, China.
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Al-khlifeh E, Khadem S, Hausmann B, Berry D. Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley. Front Microbiol 2023; 14:1258775. [PMID: 37954239 PMCID: PMC10637782 DOI: 10.3389/fmicb.2023.1258775] [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: 07/14/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023] Open
Abstract
Host phylogeny and the environment play vital roles in shaping animal microbiomes. However, the effects of these variables on the diversity and richness of the gut microbiome in different bioclimatic zones remain underexplored. In this study, we investigated the effects of host phylogeny and bioclimatic zone on the diversity and composition of the gut microbiota of two heterospecific rodent species, the spiny mouse Acomys cahirinus and the house mouse Mus musculus, in three bioclimatic zones of the African Great Rift Valley (GRV). We confirmed host phylogeny using the D-loop sequencing method and analyzed the influence of host phylogeny and bioclimatic zone parameters on the rodent gut microbiome using high-throughput amplicon sequencing of 16S rRNA gene fragments. Phylogenetic analysis supported the morphological identification of the rodents and revealed a marked genetic difference between the two heterospecific species. We found that bioclimatic zone had a significant effect on the gut microbiota composition while host phylogeny did not. Microbial alpha diversity of heterospecific hosts was highest in the Mediterranean forest bioclimatic zone, followed by the Irano-Turanian shrubland, and was lowest in the Sudanian savanna tropical zone. The beta diversity of the two rodent species showed significant differences across the Mediterranean, Irano-Turanian, and Sudanian regions. The phyla Firmicutes and Bacteroidetes were highly abundant, and Deferribacterota, Cyanobacteria and Proteobacteria were also prominent. Amplicon sequence variants (ASVs) were identified that were unique to the Sudanian bioclimatic zone. The core microbiota families recovered in this study were consistent among heterospecific hosts. However, diversity decreased in conspecific host populations found at lower altitudes in Sudanian bioclimatic zone. The composition of the gut microbiota is linked to the adaptation of the host to its environment, and this study underscores the importance of incorporating climatic factors such as elevation and ambient temperature, in empirical microbiome research and is the first to describe the rodent gut microbiome from the GRV.
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Affiliation(s)
- Enas Al-khlifeh
- Laboratory of Immunology, Department of Medical Laboratory Science, Al-Balqa Applied University, Al-Salt, Jordan
| | - Sanaz Khadem
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
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Buschi E, Dell’Anno A, Tangherlini M, Stefanni S, Lo Martire M, Núñez-Pons L, Avila C, Corinaldesi C. Rhodobacteraceae dominate the core microbiome of the sea star Odontaster validus (Koehler, 1906) in two opposite geographical sectors of the Antarctic Ocean. Front Microbiol 2023; 14:1234725. [PMID: 37799611 PMCID: PMC10548270 DOI: 10.3389/fmicb.2023.1234725] [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: 06/05/2023] [Accepted: 08/29/2023] [Indexed: 10/07/2023] Open
Abstract
Microbiota plays essential roles in the health, physiology, and in adaptation of marine multi-cellular organisms to their environment. In Antarctica, marine organisms have a wide range of unique physiological functions and adaptive strategies, useful for coping with extremely cold conditions. However, the role of microbiota associated with Antarctic organisms in such adaptive strategies is underexplored. In the present study, we investigated the diversity and putative functions of the microbiome of the sea star Odontaster validus, one of the main keystone species of the Antarctic benthic ecosystems. We compared the whole-body bacterial microbiome of sea stars from different sites of the Antarctic Peninsula and Ross Sea, two areas located in two opposite geographical sectors of the Antarctic continent. The taxonomic composition of O. validus microbiomes changed both between and within the two Antarctic sectors, suggesting that environmental and biological factors acting both at large and local scales may influence microbiome diversity. Despite this, one bacterial family (Rhodobacteraceae) was shared among all sea star individuals from the two geographical sectors, representing up to 95% of the microbial core, and suggesting a key functional role of this taxon in holobiont metabolism and well-being. In addition, the genus Roseobacter belonging to this family was also present in the surrounding sediment, implying a potential horizontal acquisition of dominant bacterial core taxa via host-selection processes from the environment.
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Affiliation(s)
- Emanuela Buschi
- Department of Marine Biotechnology, Stazione Zoologica di Napoli “Anton Dohrn”, Fano Marine Centre, Fano, Italy
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica di Napoli “Anton Dohrn”, Fano Marine Centre, Fano, Italy
| | - Sergio Stefanni
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica di Napoli “Anton Dohrn”, Naples, Italy
| | - Marco Lo Martire
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Laura Núñez-Pons
- Department of Integrative Marine Ecology, Stazione Zoologica di Napoli “Anton Dohrn”, Naples, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Conxita Avila
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat, University of Barcelona, Barcelona, Catalonia, Spain
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
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11
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Matthee CA, Bierman A, Krasnov BR, Matthee S, van der Mescht L. Documenting the microbiome diversity and distribution in selected fleas from South Africa with an emphasis on the cat flea, Ctenocephalides f. felis. Parasitology 2023; 150:979-989. [PMID: 37681253 PMCID: PMC10941216 DOI: 10.1017/s0031182023000835] [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: 03/22/2023] [Revised: 08/04/2023] [Accepted: 08/22/2023] [Indexed: 09/09/2023]
Abstract
The factors that influence parasite associated bacterial microbial diversity and the geographic distributions of bacteria are not fully understood. In an effort to gain a deeper understanding of the relationship between the bacterial diversity of Ctenocephalides fleas and host species and the external environment, we conducted a metagenetic analysis of 107 flea samples collected from 8 distinct sampling sites in South Africa. Pooled DNA samples mostly comprising of 2 or 3 individuals sampled from the same host, and belonging to the same genetic cluster, were sequenced using the Ion PGM™ Hi-Q™ Kit and the Ion 316™ Chip v2. Differences were detected in the microbiome compositions between Ctenocephalides felis, Ctenocephalides canis and Ctenocephalides connatus. Although based on a small sample, C. connatus occurring on wildlife harboured a higher bacterial richness when compared to C. felis on domestic animals. Intraspecific differences in the microbial OTU diversity were detected within C. f. felis that occurred on domestic cats and dogs. Different genetic lineages of C. f. felis were similar in microbial compositions but some differences exist in the presence or absence of rare bacteria. Rickettsia and Bartonella OTU's identified in South African cat fleas differ from those identified in the USA and Australia. Intraspecific microbial compositions also differ across geographic sampling sites. Generalized dissimilarity modelling showed that temperature and humidity are potentially important environmental factors explaining the pattern obtained.
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Affiliation(s)
- Conrad A. Matthee
- Department of Botany and Zoology, Evolutionary Genomics Group, Stellenbosch University, Stellenbosch, South Africa
| | - Anandi Bierman
- Department of Conservation Ecology & Entomology, Centre for Invasion Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Boris R. Krasnov
- Mitrani Department of Desert Ecology, Swiss Institute for Dryland Environmental and Energy Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Sonja Matthee
- Department of Conservation Ecology & Entomology, Stellenbosch University, Stellenbosch, South Africa
| | - Luther van der Mescht
- Department of Botany and Zoology, Evolutionary Genomics Group, Stellenbosch University, Stellenbosch, South Africa
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12
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Aldeguer-Riquelme B, Antón J, Santos F. Distribution, abundance, and ecogenomics of the Palauibacterales, a new cosmopolitan thiamine-producing order within the Gemmatimonadota phylum. mSystems 2023; 8:e0021523. [PMID: 37345931 PMCID: PMC10469786 DOI: 10.1128/msystems.00215-23] [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: 03/05/2023] [Accepted: 04/19/2023] [Indexed: 06/23/2023] Open
Abstract
The phylum Gemmatimonadota comprises mainly uncultured microorganisms that inhabit different environments such as soils, freshwater lakes, marine sediments, sponges, or corals. Based on 16S rRNA gene studies, the group PAUC43f is one of the most frequently retrieved Gemmatimonadota in marine samples. However, its physiology and ecological roles are completely unknown since, to date, not a single PAUC43f isolate or metagenome-assembled genome (MAG) has been characterized. Here, we carried out a broad study of the distribution, abundance, ecotaxonomy, and metabolism of PAUC43f, for which we propose the name of Palauibacterales. This group was detected in 4,965 16S rRNA gene amplicon datasets, mainly from marine sediments, sponges, corals, soils, and lakes, reaching up to 34.3% relative abundance, which highlights its cosmopolitan character, mainly salt-related. The potential metabolic capabilities inferred from 52 Palauibacterales MAGs recovered from marine sediments, sponges, and saline soils suggested a facultative aerobic and chemoorganotrophic metabolism, although some members may also oxidize hydrogen. Some Palauibacterales species might also play an environmental role as N2O consumers as well as suppliers of serine and thiamine. When compared to the rest of the Gemmatimonadota phylum, the biosynthesis of thiamine was one of the key features of the Palauibacterales. Finally, we show that polysaccharide utilization loci (PUL) are widely distributed within the Gemmatimonadota so that they are not restricted to Bacteroidetes, as previously thought. Our results expand the knowledge about this cryptic phylum and provide new insights into the ecological roles of the Gemmatimonadota in the environment. IMPORTANCE Despite advances in molecular and sequencing techniques, there is still a plethora of unknown microorganisms with a relevant ecological role. In the last years, the mostly uncultured Gemmatimonadota phylum is attracting scientific interest because of its widespread distribution and abundance, but very little is known about its ecological role in the marine ecosystem. Here we analyze the global distribution and potential metabolism of the marine Gemmatimonadota group PAUC43f, for which we propose the name of Palauibacterales order. This group presents a saline-related character and a chemoorganoheterotrophic and facultatively aerobic metabolism, although some species might oxidize H2. Given that Palauibacterales is potentially able to synthesize thiamine, whose auxotrophy is the second most common in the marine environment, we propose Palauibacterales as a key thiamine supplier to the marine communities. This finding suggests that Gemmatimonadota could have a more relevant role in the marine environment than previously thought.
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Affiliation(s)
- Borja Aldeguer-Riquelme
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute of Environmental Studies Ramón Margalef, University of Alicante, Alicante, Spain
| | - Fernando Santos
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
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13
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Vadillo Gonzalez S, Vranken S, Coleman MA, Wernberg T, Steinberg PD, Marzinelli EM. Host genotype and microbiome associations in co-occurring clonal and non-clonal kelp, Ecklonia radiata. Mol Ecol 2023; 32:4584-4598. [PMID: 37332135 DOI: 10.1111/mec.17056] [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: 10/25/2022] [Revised: 04/21/2023] [Accepted: 06/09/2023] [Indexed: 06/20/2023]
Abstract
A fundamental question in holobiont biology is the extent to which microbiomes are determined by host characteristics regulated by their genotype. Studies on the interactions of host genotype and microbiomes are emerging but disentangling the role that host genotype has in shaping microbiomes remains challenging in natural settings. Host genotypes tend to be segregated in space and affected by different environments. Here we overcome this challenge by studying an unusual situation where host asexual (5 clonal lineages) and sexual genotypes (15 non-clonal lineages) of the same species co-occur under the same environment. This allowed us to partition the influence of morphological traits and genotype in shaping host-associated bacterial communities. Lamina-associated bacteria of co-occurring kelp sexual non-clonal (Ecklonia radiata) and asexual clonal (E. brevipes) morphs were compared to test whether host genotype influences microbiomes beyond morphology. Similarity of bacterial composition and predicted functions were evaluated among individuals within a single clonal genotype or among non-clonal genotypes of each morph. Higher similarity in bacterial composition and inferred functions were found among identical clones of E. brevipes compared to other clonal genotypes or unique non-clonal E. radiata genotypes. Additionally, bacterial diversity and composition differed significantly between the two morphs and were related with one morphological trait in E. brevipes (haptera). Thus, factors regulated by the host genotype (e.g. secondary metabolite production) likely drive differences in microbial communities between morphs. The strong association of genotype and microbiome found here highlights the importance of genetic relatedness of hosts in determining variability in their bacterial symbionts.
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Affiliation(s)
- Sebastian Vadillo Gonzalez
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
| | - Sofie Vranken
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
| | - Melinda A Coleman
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
- New South Wales Fisheries, Department of Primary Industries, National Marine Science Centre, Coffs Harbour, New South Wales, Australia
| | - Thomas Wernberg
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
- Institute of Marine Research, Floedevigen Research Station, His, Norway
| | - Peter D Steinberg
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ezequiel M Marzinelli
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
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14
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Jespersen ML, Munk P, Johansen J, Kaas RS, Webel H, Vigre H, Nielsen HB, Rasmussen S, Aarestrup FM. Global within-species phylogenetics of sewage microbes suggest that local adaptation shapes geographical bacterial clustering. Commun Biol 2023; 6:700. [PMID: 37422584 PMCID: PMC10329687 DOI: 10.1038/s42003-023-05083-8] [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: 06/01/2022] [Accepted: 06/28/2023] [Indexed: 07/10/2023] Open
Abstract
Most investigations of geographical within-species differences are limited to focusing on a single species. Here, we investigate global differences for multiple bacterial species using a dataset of 757 metagenomics sewage samples from 101 countries worldwide. The within-species variations were determined by performing genome reconstructions, and the analyses were expanded by gene focused approaches. Applying these methods, we recovered 3353 near complete (NC) metagenome assembled genomes (MAGs) encompassing 1439 different MAG species and found that within-species genomic variation was in 36% of the investigated species (12/33) coherent with regional separation. Additionally, we found that variation of organelle genes correlated less with geography compared to metabolic and membrane genes, suggesting that the global differences of these species are caused by regional environmental selection rather than dissemination limitations. From the combination of the large and globally distributed dataset and in-depth analysis, we present a wide investigation of global within-species phylogeny of sewage bacteria. The global differences found here emphasize the need for worldwide data sets when making global conclusions.
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Affiliation(s)
- Marie Louise Jespersen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Joachim Johansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Clinical-Microbiomics A/S, Copenhagen, Denmark
| | - Rolf Sommer Kaas
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Henry Webel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Håkan Vigre
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
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15
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Roveta C, Calcinai B, Girolametti F, Fernandes Couceiro J, Puce S, Annibaldi A, Costa R. The prokaryotic community of Chondrosia reniformis Nardo, 1847: from diversity to mercury detection. ZOOLOGY 2023; 158:126091. [PMID: 37003141 DOI: 10.1016/j.zool.2023.126091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 02/21/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023]
Abstract
Microbial communities inhabiting sponges are known to take part in many metabolic pathways, including nutrient cycles, and possibly also in the bioaccumulation of trace elements (TEs). Here, we used high-throughput, Illumina sequencing of 16S rRNA genes to characterize the prokaryotic communities present in the cortex and choanosome, respectively the external and internal body region of Chondrosia reniformis, and in the surrounding seawater. Furthermore, we estimated the total mercury content (THg) in these body regions of the sponge and in the corresponding microbial cell pellets. Fifteen prokaryotic phyla were detected in association with C. reniformis, 13 belonging to the domain Bacteria and two to the Archaea. No significant differences between the prokaryotic community composition of the two regions were found. Three lineages of ammonium-oxidizing organisms (Cenarchaeum symbiosum, Nitrosopumilus maritimus, and Nitrosococcus sp.) co-dominated the prokaryotic community, suggesting ammonium oxidation/nitrification as a key metabolic pathway within the microbiome of C. reniformis. In the sponge fractions, higher THg levels were found in the choanosome compared to the cortex. In contrast, comparable THg levels found in the microbial pellets obtained from both regions were significantly lower than those observed in the corresponding sponge fractions. Our work provides new insights into the prokaryotic communities and TEs distribution in different body parts of a model organism relevant for marine conservation and biotechnology. In this sense, this study paves the way for scientists to deepen the possible application of sponges not only as bioindicators, but also as bioremediation tools of metal polluted environments.
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Affiliation(s)
- Camilla Roveta
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
| | - Barbara Calcinai
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Federico Girolametti
- Department of Industrial Engineering and Mathematical Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Joana Fernandes Couceiro
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Stefania Puce
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Anna Annibaldi
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Centre of Marine Sciences (CCMAR), University of Algarve, Portugal
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16
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Kardish MR, Stachowicz JJ. Local environment drives rapid shifts in composition and phylogenetic clustering of seagrass microbiomes. Sci Rep 2023; 13:3673. [PMID: 36871071 PMCID: PMC9985655 DOI: 10.1038/s41598-023-30194-x] [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: 07/06/2022] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
Plant microbiomes depend on environmental conditions, stochasticity, host species, and genotype identity. Eelgrass (Zostera marina) is a unique system for plant-microbe interactions as a marine angiosperm growing in a physiologically-challenging environment with anoxic sediment, periodic exposure to air at low tide, and fluctuations in water clarity and flow. We tested the influence of host origin versus environment on eelgrass microbiome composition by transplanting 768 plants among four sites within Bodega Harbor, CA. Over three months following transplantation, we sampled microbial communities monthly on leaves and roots and sequenced the V4-V5 region of the 16S rRNA gene to assess community composition. The main driver of leaf and root microbiome composition was destination site; more modest effects of host origin site did not last longer than one month. Community phylogenetic analyses suggested that environmental filtering structures these communities, but the strength and nature of this filtering varies among sites and over time and roots and leaves show opposing gradients in clustering along a temperature gradient. We demonstrate that local environmental differences create rapid shifts in associated microbial community composition with potential functional implications for rapid host acclimation under shifting environmental conditions.
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Affiliation(s)
- Melissa R Kardish
- Department of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA, 95616, USA. .,Center for Population Biology, University of California, One Shields Avenue, Davis, CA, 95616, USA.
| | - John J Stachowicz
- Department of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA, 95616, USA.,Center for Population Biology, University of California, One Shields Avenue, Davis, CA, 95616, USA
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17
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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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18
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Burgunter-Delamare B, Rousvoal S, Legeay E, Tanguy G, Fredriksen S, Boyen C, Dittami SM. The Saccharina latissima microbiome: Effects of region, season, and physiology. Front Microbiol 2023; 13:1050939. [PMID: 36687663 PMCID: PMC9858215 DOI: 10.3389/fmicb.2022.1050939] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/12/2022] [Indexed: 01/09/2023] Open
Abstract
Introduction Saccharina latissima is a canopy-forming species of brown algae and, as such, is considered an ecosystem engineer. Several populations of this alga are exploited worldwide, and a decrease in the abundance of S. latissima at its southern distributional range limits has been observed. Despite its economic and ecological interest, only a few data are available on the composition of microbiota associated with S. latissima and its role in algal physiologyn. Methods We studied the whole bacterial community composition associated with S. latissima samples from three locations (Brittany, Helgoland, and Skagerrak) by 16S metabarcoding analyses at different scales: algal blade part, regions, season (at one site), and algal physiologic state. Results and Discussion We have shown that the difference in bacterial composition is driven by factors of decreasing importance: (i) the algal tissues (apex/meristem), (ii) the geographical area, (iii) the seasons (at the Roscoff site), and (iv) the algal host's condition (healthy vs. symptoms). Overall, Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia dominated the general bacterial communities. Almost all individuals hosted bacteria of the genus Granulosicoccus, accounting for 12% of the total sequences, and eight additional core genera were identified. Our results also highlight a microbial signature characteristic for algae in poor health independent of the disease symptoms. Thus, our study provides a comprehensive overview of the S. latissima microbiome, forming a basis for understanding holobiont functioning.
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Affiliation(s)
- Bertille Burgunter-Delamare
- CNRS, Sorbonne Université, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Roscoff, France,*Correspondence: Bertille Burgunter-Delamare,
| | - Sylvie Rousvoal
- CNRS, Sorbonne Université, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Roscoff, France
| | - Erwan Legeay
- FR2424 Station Biologique de Roscoff, CNRS, Sorbonne Université, Roscoff, France
| | - Gwenn Tanguy
- FR2424 Station Biologique de Roscoff, CNRS, Sorbonne Université, Roscoff, France
| | | | - Catherine Boyen
- CNRS, Sorbonne Université, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Roscoff, France,FR2424 Station Biologique de Roscoff, CNRS, Sorbonne Université, Roscoff, France
| | - Simon M. Dittami
- CNRS, Sorbonne Université, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Roscoff, France,Simon M. Dittami,
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19
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Bridson C, Vellaniparambil L, Antwis RE, Müller W, Gilman RT, Rowntree JK. Genetic diversity of honeybee colonies predicts gut bacterial diversity of individual colony members. Environ Microbiol 2022; 24:5643-5653. [PMID: 35920034 PMCID: PMC10087737 DOI: 10.1111/1462-2920.16150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/18/2022] [Accepted: 07/22/2022] [Indexed: 01/13/2023]
Abstract
The gut microbiota of social bees is relatively simple and dominated by a set of core taxa found consistently in individuals around the world. Yet, variation remains and can affect host health. We characterized individual- and regional-scale variation in honeybee (Apis mellifera) gut microbiota from 64 colonies in North-West England by sequencing the V4 region of the 16S rRNA gene and asked whether microbiota were influenced by host genotype and landscape composition. We also characterized the genotypes of individual bees and the land cover surrounding each colony. The literature-defined core taxa dominated across the region despite the varied environments. However, there was variation in the relative abundance of core taxa, and colony membership explained much of this variation. Individuals from more genetically diverse colonies had more diverse microbiotas, but individual genetic diversity did not influence gut microbial diversity. There were weak trends for colonies in more similar landscapes to have more similar microbiota, and for bees from more urban landscapes to have less diverse microbiota. To our knowledge, this is the first report for any species that the gut bacterial communities of individuals are influenced by the genotypes of others in the population.
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Affiliation(s)
- Calum Bridson
- Faculty of Science and Engineering, University of Manchester, Manchester, UK.,Faculty of Biology Medicine and Health, Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK.,Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany.,Translational Lung Research Centre (TLRC), Heidelberg, Germany
| | - Latha Vellaniparambil
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
| | - Rachel E Antwis
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Werner Müller
- Faculty of Biology Medicine and Health, Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK.,Miltenyi Biotec, Bergisch Gladbach, Germany
| | - R Tucker Gilman
- Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Jennifer K Rowntree
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
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20
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Scherer BP, Mast A. Red Mangrove Propagule Bacterial Communities Vary With Geographic, But Not Genetic Distance. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02147-w. [PMID: 36441249 DOI: 10.1007/s00248-022-02147-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/12/2022] [Indexed: 06/16/2023]
Abstract
Bacterial communities associated with plant propagules remain understudied, despite the opportunities that propagules represent as dispersal vectors for bacteria to new sites. These communities may be the product of a combination of environmental influence and inheritance from parent to offspring. The relative role of these mechanisms could have significant implications for our understanding of plant-microbe interactions. We studied the correlates of microbiome community similarities across an invasion front of red mangroves (Rhizophora mangle L.) in Florida, where the species is expanding northward. We collected georeferenced propagule samples from 110 individuals of red mangroves across 11 populations in Florida and used 16S rRNA gene (iTag) sequencing to describe their bacterial communities. We found no core community of bacterial amplicon sequence variants (ASVs) across the Florida range of red mangroves, though there were some ASVs shared among individuals within most populations. Populations differed significantly as measured by Bray-Curtis dissimilarity, but not Unifrac distance. We generated data from 6 microsatellite loci from 60 individuals across 9 of the 11 populations. Geographic distance was correlated with beta diversity, but genetic distance was not. We conclude that red mangrove propagule bacterial communities are likely influenced more by local environmental acquisition than by inheritance.
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Affiliation(s)
- Brendan P Scherer
- Department of Biological Science, Florida State University, King Life Sciences Building, 319 Stadium Drive, Tallahassee, Fl, 32304, USA.
| | - Austin Mast
- Department of Biological Science, Florida State University, King Life Sciences Building, 319 Stadium Drive, Tallahassee, Fl, 32304, USA
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21
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Sugden S, Holert J, Cardenas E, Mohn WW, Stein LY. Microbiome of the freshwater sponge Ephydatia muelleri shares compositional and functional similarities with those of marine sponges. THE ISME JOURNAL 2022; 16:2503-2512. [PMID: 35906397 PMCID: PMC9562138 DOI: 10.1038/s41396-022-01296-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/27/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Sponges are known for hosting diverse communities of microbial symbionts, but despite persistent interest in the sponge microbiome, most research has targeted marine sponges; freshwater sponges have been the focus of less than a dozen studies. Here, we used 16 S rRNA gene amplicon sequencing and shotgun metagenomics to characterize the microbiome of the freshwater sponge Ephydatia muelleri and identify potential indicators of sponge-microbe mutualism. Using samples collected from the Sooke, Nanaimo, and Cowichan Rivers on Vancouver Island, British Columbia, we show that the E. muelleri microbiome is distinct from the ambient water and adjacent biofilms and is dominated by Sediminibacterium, Comamonas, and unclassified Rhodospirillales. We also observed phylotype-level differences in sponge microbiome taxonomic composition among different rivers. These differences were not reflected in the ambient water, suggesting that other environmental or host-specific factors may drive the observed geographic variation. Shotgun metagenomes and metagenome-assembled genomes further revealed that freshwater sponge-associated bacteria share many genomic similarities with marine sponge microbiota, including an abundance of defense-related proteins (CRISPR, restriction-modification systems, and transposases) and genes for vitamin B12 production. Overall, our results provide foundational information on the composition and function of freshwater sponge-associated microbes, which represent an important yet underappreciated component of the global sponge microbiome.
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Affiliation(s)
- Scott Sugden
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
- Department of Natural Resource Sciences, McGill University, Montreal, QC, Canada.
| | - Johannes Holert
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Erick Cardenas
- Department of Microbiology and Immunology, Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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22
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Díez-Vives C, Koutsouveli V, Conejero M, Riesgo A. Global patterns in symbiont selection and transmission strategies in sponges. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1015592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sponges host dense and diverse communities of microbes (known as the microbiome) beneficial for the host nutrition and defense. Symbionts in turn receive shelter and metabolites from the sponge host, making their relationship beneficial for both partners. Given that sponge-microbes associations are fundamental for the survival of both, especially the sponge, such relationship is maintained through their life and even passed on to the future generations. In many organisms, the microbiome has profound effects on the development of the host, but the influence of the microbiome on the reproductive and developmental pathways of the sponges are less understood. In sponges, microbes are passed on to oocytes, sperm, embryos, and larvae (known as vertical transmission), using a variety of methods that include direct uptake from the mesohyl through phagocytosis by oocytes to indirect transmission to the oocyte by nurse cells. Such microbes can remain in the reproductive elements untouched, for transfer to offspring, or can be digested to make the yolky nutrient reserves of oocytes and larvae. When and how those decisions are made are fundamentally unanswered questions in sponge reproduction. Here we review the diversity of vertical transmission modes existent in the entire phylum Porifera through detailed imaging using electron microscopy, available metabarcoding data from reproductive elements, and macroevolutionary patterns associated to phylogenetic constraints. Additionally, we examine the fidelity of this vertical transmission and possible reasons for the observed variability in some developmental stages. Our current understanding in marine sponges, however, is that the adult microbial community is established by a combination of both vertical and horizontal (acquisition from the surrounding environment in each new generation) transmission processes, although the extent in which each mode shapes the adult microbiome still remains to be determined. We also assessed the fundamental role of filtration, the cellular structures for acquiring external microbes, and the role of the host immune system, that ultimately shapes the stable communities of prokaryotes observed in adult sponges.
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23
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Kelly JB, Carlson DE, Low JS, Thacker RW. Novel trends of genome evolution in highly complex tropical sponge microbiomes. MICROBIOME 2022; 10:164. [PMID: 36195901 PMCID: PMC9531527 DOI: 10.1186/s40168-022-01359-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/03/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Tropical members of the sponge genus Ircinia possess highly complex microbiomes that perform a broad spectrum of chemical processes that influence host fitness. Despite the pervasive role of microbiomes in Ircinia biology, it is still unknown how they remain in stable association across tropical species. To address this question, we performed a comparative analysis of the microbiomes of 11 Ircinia species using whole-metagenomic shotgun sequencing data to investigate three aspects of bacterial symbiont genomes-the redundancy in metabolic pathways across taxa, the evolution of genes involved in pathogenesis, and the nature of selection acting on genes relevant to secondary metabolism. RESULTS A total of 424 new, high-quality bacterial metagenome-assembled genomes (MAGs) were produced for 10 Caribbean Ircinia species, which were evaluated alongside 113 publicly available MAGs sourced from the Pacific species Ircinia ramosa. Evidence of redundancy was discovered in that the core genes of several primary metabolic pathways could be found in the genomes of multiple bacterial taxa. Across hosts, the metagenomes were depleted in genes relevant to pathogenicity and enriched in eukaryotic-like proteins (ELPs) that likely mimic the hosts' molecular patterning. Finally, clusters of steroid biosynthesis genes (CSGs), which appear to be under purifying selection and undergo horizontal gene transfer, were found to be a defining feature of Ircinia metagenomes. CONCLUSIONS These results illustrate patterns of genome evolution within highly complex microbiomes that illuminate how associations with hosts are maintained. The metabolic redundancy within the microbiomes could help buffer the hosts from changes in the ambient chemical and physical regimes and from fluctuations in the population sizes of the individual microbial strains that make up the microbiome. Additionally, the enrichment of ELPs and depletion of LPS and cellular motility genes provide a model for how alternative strategies to virulence can evolve in microbiomes undergoing mixed-mode transmission that do not ultimately result in higher levels of damage (i.e., pathogenicity) to the host. Our last set of results provides evidence that sterol biosynthesis in Ircinia-associated bacteria is widespread and that these molecules are important for the survival of bacteria in highly complex Ircinia microbiomes. Video Abstract.
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Affiliation(s)
- Joseph B Kelly
- Aquatic Ecology and Evolution, Limnological Institute University Konstanz, Konstanz, Germany.
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA.
| | - David E Carlson
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Jun Siong Low
- Institute of Microbiology,ETH Zürich, Zürich, Switzerland
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Robert W Thacker
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Panama City, Republic of Panama
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24
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Cleary DFR, Polónia ARM, Swierts T, Coelho FJRC, de Voogd NJ, Gomes NCM. Spatial and environmental variables structure sponge symbiont communities. Mol Ecol 2022; 31:4932-4948. [PMID: 35881675 PMCID: PMC9804187 DOI: 10.1111/mec.16631] [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: 06/11/2021] [Revised: 05/13/2022] [Accepted: 07/08/2022] [Indexed: 01/05/2023]
Abstract
Understanding the maintenance and origin of beta diversity is a central topic in ecology. However, the factors that drive diversity patterns and underlying processes remain unclear, particularly for host-prokaryotic associations. Here, beta diversity patterns were studied in five prokaryotic biotopes, namely, two high microbial abundance (HMA) sponge taxa (Xestospongia spp. and Hyrtios erectus), one low microbial abundance (LMA) sponge taxon (Stylissa carteri), sediment and seawater sampled across thousands of kilometres. Using multiple regression on distance matrices (MRM), spatial (geographic distance) and environmental (sea surface temperature and chlorophyll α concentrations) variables proved significant predictors of beta diversity in all five biotopes and together explained from 54% to 82% of variation in dissimilarity of both HMA species, 27% to 43% of variation in sediment and seawater, but only 20% of variation of the LMA S. carteri. Variance partitioning was subsequently used to partition the variation into purely spatial, purely environmental and spatially-structured environmental components. The amount of variation in dissimilarity explained by the purely spatial component was lowest for S. carteri at 11% and highest for H. erectus at 55%. The purely environmental component, in turn, only explained from 0.15% to 2.83% of variation in all biotopes. In addition to spatial and environmental variables, a matrix of genetic differences between pairs of sponge individuals also proved a significant predictor of variation in prokaryotic dissimilarity of the Xestospongia species complex. We discuss the implications of these results for the HMA-LMA dichotomy and compare the MRM results with results obtained using constrained ordination and zeta diversity.
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Affiliation(s)
- Daniel F. R. Cleary
- CESAM ‐ Centre for Environmental and Marine Studies, Department of BiologyUniversity of AveiroAveiroPortugal
| | - Ana R. M. Polónia
- CESAM ‐ Centre for Environmental and Marine Studies, Department of BiologyUniversity of AveiroAveiroPortugal
| | - Thomas Swierts
- Marine Biodiversity, Naturalis Biodiversity CenterLeidenThe Netherlands,Institute of Environmental Sciences (CML)Leiden UniversityLeidenThe Netherlands
| | - Francisco J. R. C. Coelho
- CESAM ‐ Centre for Environmental and Marine Studies, Department of BiologyUniversity of AveiroAveiroPortugal
| | - Nicole J. de Voogd
- Marine Biodiversity, Naturalis Biodiversity CenterLeidenThe Netherlands,Institute of Environmental Sciences (CML)Leiden UniversityLeidenThe Netherlands
| | - Newton C. M. Gomes
- CESAM ‐ Centre for Environmental and Marine Studies, Department of BiologyUniversity of AveiroAveiroPortugal
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25
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Aldeguer-Riquelme B, Rubio-Portillo E, Álvarez-Rogel J, Giménez-Casalduero F, Otero XL, Belando MD, Bernardeau-Esteller J, García-Muñoz R, Forcada A, Ruiz JM, Santos F, Antón J. Factors structuring microbial communities in highly impacted coastal marine sediments (Mar Menor lagoon, SE Spain). Front Microbiol 2022; 13:937683. [PMID: 36160249 PMCID: PMC9491240 DOI: 10.3389/fmicb.2022.937683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/27/2022] [Indexed: 11/21/2022] Open
Abstract
Coastal marine lagoons are environments highly vulnerable to anthropogenic pressures such as agriculture nutrient loading or runoff from metalliferous mining. Sediment microorganisms, which are key components in the biogeochemical cycles, can help attenuate these impacts by accumulating nutrients and pollutants. The Mar Menor, located in the southeast of Spain, is an example of a coastal lagoon strongly altered by anthropic pressures, but the microbial community inhabiting its sediments remains unknown. Here, we describe the sediment prokaryotic communities along a wide range of environmental conditions in the lagoon, revealing that microbial communities were highly heterogeneous among stations, although a core microbiome was detected. The microbiota was dominated by Delta- and Gammaproteobacteria and members of the Bacteroidia class. Additionally, several uncultured groups such as Asgardarchaeota were detected in relatively high proportions. Sediment texture, the presence of Caulerpa or Cymodocea, depth, and geographic location were among the most important factors structuring microbial assemblages. Furthermore, microbial communities in the stations with the highest concentrations of potentially toxic elements (Fe, Pb, As, Zn, and Cd) were less stable than those in the non-contaminated stations. This finding suggests that bacteria colonizing heavily contaminated stations are specialists sensitive to change.
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Affiliation(s)
- Borja Aldeguer-Riquelme
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Esther Rubio-Portillo
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - José Álvarez-Rogel
- Department of Agricultural Engineering of the Escuela Técnica Superior Ingeniería Agronómica (ETSIA) & Soil Ecology and Biotechnology Unit of the Institute of Plant Biotechnology, Technical University of Cartagena, Cartagena, Spain
| | | | - Xose Luis Otero
- Cross-Research in Environmental Technologies (CRETUS), Departamento de Edafoloxía e Química Agrícola, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - María-Dolores Belando
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Jaime Bernardeau-Esteller
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Rocío García-Muñoz
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Aitor Forcada
- Department of Marine Science and Applied Biology, University of Alicante, Alicante, Spain
| | - Juan M. Ruiz
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Fernando Santos
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute of Environmental Studies Ramón Margalef, University of Alicante, Alicante, Spain
- *Correspondence: Josefa Antón,
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26
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Chalifour BN, Elder LE, Li J. Gut microbiome of century-old snail specimens stable across time in preservation. MICROBIOME 2022; 10:99. [PMID: 35765039 PMCID: PMC9241308 DOI: 10.1186/s40168-022-01286-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/21/2022] [Indexed: 05/10/2023]
Abstract
BACKGROUND Museum biological specimens provide a unique means of gathering ecological information that spans wide temporal ranges. Museum specimens can also provide information on the microbial communities that persist within the host specimen. Together, these provide researchers valuable opportunities to study long-term trends and mechanisms of microbial community change. The effects of decades-long museum preservation on host-microbial communities have not been systematically assessed. The University of Colorado's Museum of Natural History has densely sampled Oreohelix strigosa (Rocky Mountainsnail) for the past century; many are preserved in ethanol, which provides an excellent opportunity to explore how the microbiome changes across time in preservation. RESULTS We used 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing to examine Oreohelix strigosa gut microbiomes from museum specimens across a 98-year range, as well as within short-term preservation treatments collected in 2018. Treatment groups included samples extracted fresh, without preservation; samples starved prior to extraction; and samples preserved for 1 month, 6 months, and 9 months. General microbiome composition was similar across all years. Sample groups belonging to specific years, or specific short-term treatments, showed unique associations with select bacterial taxa. Collection year was not a significant predictor of microbial richness, though unpreserved short-term treatments showed significantly higher richness than preserved treatments. While the year was a significant factor in microbiome composition, it did not explain much of the variation across samples. The location was a significant driver of community composition and explained more of the variability. CONCLUSIONS This study is the first to examine animal host-associated microbiome change across a period of nearly one century. Generally, geographic location was a greater factor in shaping gut microbiome composition, rather than a year collected. Consistent patterns across this temporal range indicate that historic specimens can answer many ecological questions surrounding the host-associated microbiome. Video Abstract.
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Affiliation(s)
- Bridget N. Chalifour
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant Street, 334 UCB, Boulder, CO 80309 USA
| | - Leanne E. Elder
- Museum of Natural History, University of Colorado Boulder, 265 UCB, Boulder, CO 80309 USA
- New Zealand Arthropod Collection, Manaaki Whenua Landcare Research, 231 Morrin Road St. Johns, Auckland, NZ 1072 New Zealand
| | - Jingchun Li
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant Street, 334 UCB, Boulder, CO 80309 USA
- Museum of Natural History, University of Colorado Boulder, 265 UCB, Boulder, CO 80309 USA
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27
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Wood G, Steinberg PD, Campbell AH, Vergés A, Coleman MA, Marzinelli EM. Host genetics, phenotype and geography structure the microbiome of a foundational seaweed. Mol Ecol 2022; 31:2189-2206. [PMID: 35104026 PMCID: PMC9540321 DOI: 10.1111/mec.16378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/18/2022] [Indexed: 12/01/2022]
Abstract
Interactions between hosts and their microbiota are vital to the functioning and resilience of macro-organisms. Critically, for hosts that play foundational roles in communities, understanding what drives host-microbiota interactions is essential for informing ecosystem restoration and conservation. We investigated the relative influence of host traits and the surrounding environment on microbial communities associated with the foundational seaweed Phyllospora comosa. We quantified 16 morphological and functional phenotypic traits, including host genetics (using 354 single nucleotide polymorphisms) and surface-associated microbial communities (using 16S rRNA gene amplicon sequencing) from 160 individuals sampled from eight sites spanning Phyllospora's entire latitudinal distribution (1,300 km). Combined, these factors explained 54% of the overall variation in Phyllospora's associated microbial community structure, much of which was related to the local environment (~32%). We found that putative "core" microbial taxa (i.e., present on all Phyllospora individuals sampled) exhibited slightly higher associations with host traits when compared to "variable" taxa (not present on all individuals). We identified several key genetic loci and phenotypic traits in Phyllospora that were strongly related to multiple microbial amplicon sequence variants, including taxa with known associations to seaweed defence, disease and tissue degradation. This information on how host-associated microbial communities vary with host traits and the environment enhances our current understanding of how "holobionts" (hosts plus their microbiota) are structured. Such understanding can be used to inform management strategies of these important and vulnerable habitats.
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Affiliation(s)
- Georgina Wood
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Centre for Marine Science and InnovationSchool of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Peter D. Steinberg
- Centre for Marine Science and InnovationSchool of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
- Sydney Institute of Marine ScienceSydneyNew South WalesAustralia
- Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingaporeSingapore
| | - Alexandra H. Campbell
- USC Seaweed Research GroupUniversity of the Sunshine CoastSunshine CoastQueenslandAustralia
| | - Adriana Vergés
- Centre for Marine Science and InnovationSchool of Biological, Earth and Environmental SciencesUNSW SydneySydneyNew South WalesAustralia
| | - Melinda A. Coleman
- Department of Primary IndustriesNational Marine Science CentreCoffs HarbourNew South WalesAustralia
| | - Ezequiel M. Marzinelli
- School of Life and Environmental SciencesThe University of SydneySydneyNew South WalesAustralia
- Sydney Institute of Marine ScienceSydneyNew South WalesAustralia
- Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingaporeSingapore
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28
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Jorge F, Dheilly NM, Froissard C, Wainwright E, Poulin R. Consistency of Bacterial Communities in a Parasitic Worm: Variation Throughout the Life Cycle and Across Geographic Space. MICROBIAL ECOLOGY 2022; 83:724-738. [PMID: 34136952 DOI: 10.1007/s00248-021-01774-z] [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: 03/21/2021] [Accepted: 05/12/2021] [Indexed: 06/12/2023]
Abstract
Microbial communities within metazoans are increasingly linked with development, health and behaviour, possibly functioning as integrated evolutionary units with the animal in which they live. This would require microbial communities to show some consistency both ontogenetically (across life stages) and geographically (among populations). We characterise the bacteriome of the parasitic trematode Philophthalmus attenuatus, which undergoes major life cycle transitions, and test whether its bacteriome remains consistent on developmental and spatial scales. Based on sequencing the prokaryotic 16S SSU rRNA gene, we compared the parasite bacteriome (i) across three life stages (rediae in snails, cercariae exiting snails, adults in birds) in one locality and (ii) among three geographic localities for rediae only. We found that each life stage harbours a bacteriome different from that of its host (except the adult stage) and the external environment. Very few bacterial taxa were shared among life stages, suggesting substantial ontogenetic turnover in bacteriome composition. Rediae from the three different localities also had different bacteriomes, with dissimilarities increasing with geographical distance. However, rediae from different localities nevertheless shared more bacterial taxa than did different life stages from the same locality. Changes in the bacteriome along the parasite's developmental history but some degree of geographical stability within a given life stage point toward non-random, stage-specific acquisition, selection and/or propagation of bacteria.
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Affiliation(s)
- Fátima Jorge
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Nolwenn M Dheilly
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
- ANSES, Agence Nationale de Sécurité Sanitaire de L'Alimentation, de l'Environnement et du Travail - Laboratoire de Ploufragan-Plouzané, Unité Génétique Virale de Biosécurité, Ploufragan, France
| | - Céline Froissard
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Eleanor Wainwright
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Robert Poulin
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
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29
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Ryu EP, Davenport ER. Host Genetic Determinants of the Microbiome Across Animals: From Caenorhabditis elegans to Cattle. Annu Rev Anim Biosci 2022; 10:203-226. [PMID: 35167316 PMCID: PMC11000414 DOI: 10.1146/annurev-animal-020420-032054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Animals harbor diverse communities of microbes within their gastrointestinal tracts. Phylogenetic relationship, diet, gut morphology, host physiology, and ecology all influence microbiome composition within and between animal clades. Emerging evidence points to host genetics as also playing a role in determining gut microbial composition within species. Here, we discuss recent advances in the study of microbiome heritability across a variety of animal species. Candidate gene and discovery-based studies in humans, mice, Drosophila, Caenorhabditis elegans, cattle, swine, poultry, and baboons reveal trends in the types of microbes that are heritable and the host genes and pathways involved in shaping the microbiome. Heritable gut microbes within a host species tend to be phylogenetically restricted. Host genetic variation in immune- and growth-related genes drives the abundances of these heritable bacteria within the gut. With only a small slice of the metazoan branch of the tree of life explored to date, this is an area rife with opportunities to shed light into the mechanisms governing host-microbe relationships.
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Affiliation(s)
- Erica P Ryu
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA; ,
| | - Emily R Davenport
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA; ,
- Huck Institutes of the Life Sciences and Institute for Computational and Data Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
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30
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Harrison XA, McDevitt AD, Dunn JC, Griffiths SM, Benvenuto C, Birtles R, Boubli JP, Bown K, Bridson C, Brooks DR, Browett SS, Carden RF, Chantrey J, Clever F, Coscia I, Edwards KL, Ferry N, Goodhead I, Highlands A, Hopper J, Jackson J, Jehle R, da Cruz Kaizer M, King T, Lea JMD, Lenka JL, McCubbin A, McKenzie J, de Moraes BLC, O'Meara DB, Pescod P, Preziosi RF, Rowntree JK, Shultz S, Silk MJ, Stockdale JE, Symondson WOC, de la Pena MV, Walker SL, Wood MD, Antwis RE. Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome. Proc Biol Sci 2021; 288:20210552. [PMID: 34403636 PMCID: PMC8370808 DOI: 10.1098/rspb.2021.0552] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/14/2021] [Indexed: 12/30/2022] Open
Abstract
Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, comparative evidence for fungi is lacking, especially in natural populations. Using data from 49 species, we present novel evidence of strong covariation between fungal and bacterial communities across the host phylogeny, indicative of recruitment by hosts for specific suites of microbes. Using co-occurrence networks, we demonstrate marked variation across host taxonomy in patterns of covariation between bacterial and fungal abundances. Host phylogeny drives differences in the overall richness of bacterial and fungal communities, but the effect of diet on richness was only evident in the mammalian gut microbiome. Sample type, tissue storage and DNA extraction method also affected bacterial and fungal community composition, and future studies would benefit from standardized approaches to sample processing. Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host-microbe interactions.
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Affiliation(s)
| | - Allan D. McDevitt
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jenny C. Dunn
- School of Life Sciences, Joseph Banks Laboratories, University of Lincoln, UK
| | - Sarah M. Griffiths
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Chiara Benvenuto
- School of Science, Engineering and Environment, University of Salford, UK
| | - Richard Birtles
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jean P. Boubli
- School of Science, Engineering and Environment, University of Salford, UK
| | - Kevin Bown
- School of Science, Engineering and Environment, University of Salford, UK
| | - Calum Bridson
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | - Darren R. Brooks
- School of Science, Engineering and Environment, University of Salford, UK
| | - Samuel S. Browett
- School of Science, Engineering and Environment, University of Salford, UK
| | - Ruth F. Carden
- School of Archaeology, University College Dublin, Ireland
- Wildlife Ecological and Osteological Consultancy, Wicklow, Ireland
| | - Julian Chantrey
- Institute of Veterinary Science, University of Liverpool, UK
| | - Friederike Clever
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
- Smithsonian Tropical Research Institute, Ancon, Republic of Panama
| | - Ilaria Coscia
- School of Science, Engineering and Environment, University of Salford, UK
| | - Katie L. Edwards
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, UK
| | - Natalie Ferry
- School of Science, Engineering and Environment, University of Salford, UK
| | - Ian Goodhead
- School of Science, Engineering and Environment, University of Salford, UK
| | - Andrew Highlands
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jane Hopper
- The Aspinall Foundation, Port Lympne Reserve, Hythe, Kent, UK
| | - Joseph Jackson
- School of Science, Engineering and Environment, University of Salford, UK
| | - Robert Jehle
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Tony King
- The Aspinall Foundation, Port Lympne Reserve, Hythe, Kent, UK
- School of Anthropology and Conservation, University of Kent, UK
| | - Jessica M. D. Lea
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | - Jessica L. Lenka
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Jack McKenzie
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Denise B. O'Meara
- School of Science and Computing, Waterford Institute of Technology, Ireland
| | - Poppy Pescod
- School of Science, Engineering and Environment, University of Salford, UK
| | - Richard F. Preziosi
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Jennifer K. Rowntree
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Susanne Shultz
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | | | - Jennifer E. Stockdale
- School of Biosciences, University of Cardiff, UK
- School of Life Sciences, University of Nottingham, UK
| | | | | | - Susan L. Walker
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, UK
| | - Michael D. Wood
- School of Science, Engineering and Environment, University of Salford, UK
| | - Rachael E. Antwis
- School of Science, Engineering and Environment, University of Salford, UK
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Ben-Dor Cohen E, Ilan M, Yarden O. The Culturable Mycobiome of Mesophotic Agelas oroides: Constituents and Changes Following Sponge Transplantation to Shallow Water. J Fungi (Basel) 2021; 7:jof7070567. [PMID: 34356947 PMCID: PMC8307482 DOI: 10.3390/jof7070567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022] Open
Abstract
Marine sponges harbor a diverse array of microorganisms and the composition of the microbial community has been suggested to be linked to holo-biont health. Most of the attention concerning sponge mycobiomes has been given to sponges present in shallow depths. Here, we describe the presence of 146 culturable mycobiome taxa isolated from mesophotic niche (100 m depth)-inhabiting samples of Agelas oroides, in the Mediterranean Sea. We identify some potential in vitro interactions between several A. oroides-associated fungi and show that sponge meso-hyl extract, but not its predominantly collagen-rich part, is sufficient to support hyphal growth. We demonstrate that changes in the diversity of culturable mycobiome constituents occur following sponge transplantation from its original mesophotic habitat to shallow (10 m) waters, where historically (60 years ago) this species was found. We conclude that among the 30 fungal genera identified as associated with A. oroides, Aspergillus, Penicillium and Trichoderma constitute the core mycobiome of A. oroides, and that they persist even when the sponge is transplanted to a suboptimal environment, indicative of the presence of constant, as well as dynamic, components of the sponge mycobiome. Other genera seemed more depth-related and appeared or disappeared upon host's transfer from 100 to 10 m.
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Affiliation(s)
- Eyal Ben-Dor Cohen
- School of Zoology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel; (E.B.-D.C.); (M.I.)
- Department of Plant Pathology and Microbiology, The RH Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Micha Ilan
- School of Zoology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel; (E.B.-D.C.); (M.I.)
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The RH Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
- Correspondence:
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32
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Mallott EK, Amato KR. Host specificity of the gut microbiome. Nat Rev Microbiol 2021; 19:639-653. [PMID: 34045709 DOI: 10.1038/s41579-021-00562-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2021] [Indexed: 02/07/2023]
Abstract
Developing general principles of host-microorganism interactions necessitates a robust understanding of the eco-evolutionary processes that structure microbiota. Phylosymbiosis, or patterns of microbiome composition that can be predicted by host phylogeny, is a unique framework for interrogating these processes. Identifying the contexts in which phylosymbiosis does and does not occur facilitates an evaluation of the relative importance of different ecological processes in shaping the microbial community. In this Review, we summarize the prevalence of phylosymbiosis across the animal kingdom on the basis of the current literature and explore the microbial community assembly processes and related host traits that contribute to phylosymbiosis. We find that phylosymbiosis is less prevalent in taxonomically richer microbiomes and hypothesize that this pattern is a result of increased stochasticity in the assembly of complex microbial communities. We also note that despite hosting rich microbiomes, mammals commonly exhibit phylosymbiosis. We hypothesize that this pattern is a result of a unique combination of mammalian traits, including viviparous birth, lactation and the co-evolution of haemochorial placentas and the eutherian immune system, which compound to ensure deterministic microbial community assembly. Examining both the individual and the combined importance of these traits in driving phylosymbiosis provides a new framework for research in this area moving forward.
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Affiliation(s)
- Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, IL, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA.
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33
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Davis KM, Mazel F, Parfrey LW. The microbiota of intertidal macroalgae Fucus distichus is site-specific and resistant to change following transplant. Environ Microbiol 2021; 23:2617-2631. [PMID: 33817918 DOI: 10.1111/1462-2920.15496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 01/04/2023]
Abstract
It is unclear how host-associated microbial communities will be affected by future environmental change. Characterizing how microbiota differ across sites with varying environmental conditions and assessing the stability of the microbiota in response to abiotic variation are critical steps towards predicting outcomes of environmental change. Intertidal organisms are valuable study systems because they experience extreme variation in environmental conditions on tractable timescales such as tide cycles and across small spatial gradients in the intertidal zone. Here we show a widespread intertidal macroalgae, Fucus distichus, hosts site-specific microbiota over small (meters to kilometres) spatial scales. We demonstrate stability of site-specific microbial associations by manipulating the host environment and microbial species pool with common garden and reciprocal transplant experiments. We hypothesized that F. distichus microbiota would readily shift to reflect the contemporary environment due to selective filtering by abiotic conditions and/or colonization by microbes from the new environment or nearby hosts. Instead, F. distichus microbiota was stable for days after transplantation in both the laboratory and field. Our findings expand the current understanding of microbiota dynamics on an intertidal foundation species. These results may also point to adaptations for withstanding short-term environmental variation, in hosts and/or microbes, facilitating stable host-microbial associations.
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Affiliation(s)
- Katherine M Davis
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Hakai Institute, PO Box 309, Heriot Bay, BC, V0P 1H0, Canada
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34
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Kelly JB, Carlson DE, Low JS, Rice T, Thacker RW. The Relationship Between Microbiomes and Selective Regimes in the Sponge Genus Ircinia. Front Microbiol 2021; 12:607289. [PMID: 33776953 PMCID: PMC7990798 DOI: 10.3389/fmicb.2021.607289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/18/2021] [Indexed: 01/17/2023] Open
Abstract
Sponges are often densely populated by microbes that benefit their hosts through nutrition and bioactive secondary metabolites; however, sponges must simultaneously contend with the toxicity of microbes and thwart microbial overgrowth. Despite these fundamental tenets of sponge biology, the patterns of selection in the host sponges' genomes that underlie tolerance and control of their microbiomes are still poorly understood. To elucidate these patterns of selection, we performed a population genetic analysis on multiple species of Ircinia from Belize, Florida, and Panama using an F ST -outlier approach on transcriptome-annotated RADseq loci. As part of the analysis, we delimited species boundaries among seven growth forms of Ircinia. Our analyses identified balancing selection in immunity genes that have implications for the hosts' tolerance of high densities of microbes. Additionally, our results support the hypothesis that each of the seven growth forms constitutes a distinct Ircinia species that is characterized by a unique microbiome. These results illuminate the evolutionary pathways that promote stable associations between host sponges and their microbiomes, and that potentially facilitate ecological divergence among Ircinia species.
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Affiliation(s)
- Joseph B. Kelly
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, United States
- Limnological Institute University Konstanz, Aquatic Ecology and Evolution, Konstanz, Germany
| | - David E. Carlson
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, United States
| | - Jun Siong Low
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, United States
| | - Tyler Rice
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, United States
| | - Robert W. Thacker
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, United States
- Smithsonian Tropical Research Institute, Balboa, Panama
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35
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Bulteel L, Houwenhuyse S, Declerck SAJ, Decaestecker E. The Role of Microbiome and Genotype in Daphnia magna upon Parasite Re-Exposure. Genes (Basel) 2021; 12:70. [PMID: 33430247 PMCID: PMC7825712 DOI: 10.3390/genes12010070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/31/2020] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
Recently, it has been shown that the community of gut microorganisms plays a crucial role in host performance with respect to parasite tolerance. Knowledge, however, is lacking on the role of the gut microbiome in mediating host tolerance after parasite re-exposure, especially considering multiple parasite infections. We here aimed to fill this knowledge gap by studying the role of the gut microbiome on tolerance in Daphnia magna upon multiple parasite species re-exposure. Additionally, we investigated the role of the host genotype in the interaction between the gut microbiome and the host phenotypic performance. A microbiome transplant experiment was performed in which three germ-free D. magna genotypes were exposed to a gut microbial inoculum and a parasite community treatment. The gut microbiome inocula were pre-exposed to the same parasite communities or a control treatment. Daphnia performance was monitored, and amplicon sequencing was performed to characterize the gut microbial community. Our experimental results showed that the gut microbiome plays no role in Daphnia tolerance upon parasite re-exposure. We did, however, find a main effect of the gut microbiome on Daphnia body size reflecting parasite specific responses. Our results also showed that it is rather the Daphnia genotype, and not the gut microbiome, that affected parasite-induced host mortality. Additionally, we found a role of the genotype in structuring the gut microbial community, both in alpha diversity as in the microbial composition.
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Affiliation(s)
- Lore Bulteel
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven-Campus Kulak, E. Sabbelaan 53, 8500 Kortrijk, Belgium; (S.H.); (E.D.)
| | - Shira Houwenhuyse
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven-Campus Kulak, E. Sabbelaan 53, 8500 Kortrijk, Belgium; (S.H.); (E.D.)
| | - Steven A. J. Declerck
- Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6700 AB Wageningen, The Netherlands;
- Laboratory of Aquatic Ecology, Evolution and Conservation, Department of Biology, KULeuven, 3000 Leuven, Belgium
| | - Ellen Decaestecker
- Laboratory of Aquatic Biology, Department of Biology, University of Leuven-Campus Kulak, E. Sabbelaan 53, 8500 Kortrijk, Belgium; (S.H.); (E.D.)
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de Oliveira BFR, Freitas-Silva J, Sánchez-Robinet C, Laport MS. Transmission of the sponge microbiome: moving towards a unified model. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:619-638. [PMID: 33048474 DOI: 10.1111/1758-2229.12896] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 06/11/2023]
Abstract
Sponges have co-evolved for millions of years alongside several types of microorganisms, which aside from participating in the animal's diet, are mostly symbionts. Since most of the genetic repertoire in the holobiont genome is provided by microbes, it is expected that the host-associated microbiome will be at least partially heritable. Sponges can therefore acquire their symbionts in different ways. Both vertical transmission (VT) and horizontal transmission (HT) have different advantages and disadvantages in the life cycle of these invertebrates. However, a third mode of transmission, called leaky vertical transmission or mixed mode of transmission (MMT), which incorporates both VT and HT modes, has gained relevance and seems to be the most robust model. In that regard, the aim of this review is to present the evolving knowledge on these main modes of transmission of the sponge microbiome. Our conclusions lead us to suggest that MMT may be more common for all sponges, with its frequency varying across the transmission spectrum between species and the environment. This hybrid model supports the stable and specific transmission of these microbial partners and reinforces their assistance in the resilience of sponges over the years.
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Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Jéssyca Freitas-Silva
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Claudia Sánchez-Robinet
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590, Rio de Janeiro, Brazil
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37
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Fleischer R, Risely A, Hoeck PEA, Keller LF, Sommer S. Mechanisms governing avian phylosymbiosis: Genetic dissimilarity based on neutral and MHC regions exhibits little relationship with gut microbiome distributions of Galápagos mockingbirds. Ecol Evol 2020; 10:13345-13354. [PMID: 33304542 PMCID: PMC7713960 DOI: 10.1002/ece3.6934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/14/2020] [Accepted: 09/28/2020] [Indexed: 01/01/2023] Open
Abstract
The gut microbiome of animals, which serves important functions but can also contain potential pathogens, is to varying degrees under host genetic control. This can generate signals of phylosymbiosis, whereby gut microbiome composition matches host phylogenetic structure. However, the genetic mechanisms that generate phylosymbiosis and the scale at which they act remain unclear. Two non-mutually exclusive hypotheses are that phylosymbiosis is driven by immunogenetic regions such as the major histocompatibility complex (MHC) controlling microbial composition, or by spatial structuring of neutral host genetic diversity via founder effects, genetic drift, or isolation by distance. Alternatively, associations between microbes and host phylogeny may be generated by their spatial autocorrelation across landscapes, rather than the direct effects of host genetics. In this study, we collected MHC, microsatellite, and gut microbiome data from separate individuals belonging to the Galápagos mockingbird species complex, which consists of four allopatrically distributed species. We applied multiple regression with distance matrices and Bayesian inference to test for correlations between average genetic and microbiome similarity across nine islands for which all three levels of data were available. Clustering of individuals by species was strongest when measured with microsatellite markers and weakest for gut microbiome distributions, with intermediate clustering of MHC allele frequencies. We found that while correlations between island-averaged gut microbiome composition and both microsatellite and MHC dissimilarity existed across species, these relationships were greatly weakened when accounting for geographic distance. Overall, our study finds little support for large-scale control of gut microbiome composition by neutral or adaptive genetic regions across closely related bird phylogenies, although this does not preclude the possibility that host genetics shapes gut microbiome at the individual level.
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Affiliation(s)
- Ramona Fleischer
- Institute of Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
| | - Alice Risely
- Institute of Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
| | | | - Lukas F. Keller
- Zoological MuseumUniversity of ZurichZurichSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation GenomicsUniversity of UlmUlmGermany
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38
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Díez‐Vives C, Taboada S, Leiva C, Busch K, Hentschel U, Riesgo A. On the way to specificity - Microbiome reflects sponge genetic cluster primarily in highly structured populations. Mol Ecol 2020; 29:4412-4427. [PMID: 32931063 PMCID: PMC7756592 DOI: 10.1111/mec.15635] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/21/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022]
Abstract
Most animals, including sponges (Porifera), have species-specific microbiomes. Which genetic or environmental factors play major roles structuring the microbial community at the intraspecific level in sponges is, however, largely unknown. In this study, we tested whether geographic location or genetic structure of conspecific sponges influences their microbial assembly. For that, we used three sponge species with different rates of gene flow, and collected samples along their entire distribution range (two from the Mediterranean and one from the Southern Ocean) yielding a total of 393 samples. These three sponge species have been previously analysed by microsatellites or single nucleotide polymorphisms, and here we investigate their microbiomes by amplicon sequencing of the microbial 16S rRNA gene. The sponge Petrosia ficiformis, with highly isolated populations (low gene flow), showed a stronger influence of the host genetic distance on the microbial composition than the spatial distance. Host-specificity was therefore detected at the genotypic level, with individuals belonging to the same host genetic cluster harbouring more similar microbiomes than distant ones. On the contrary, the microbiome of Ircinia fasciculata and Dendrilla antarctica - both with weak population structure (high gene flow) - seemed influenced by location rather than by host genetic distance. Our results suggest that in sponge species with high population structure, the host genetic cluster influence the microbial community more than the geographic location.
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Affiliation(s)
| | - Sergi Taboada
- Departamento de Ciencias de la VidaEU‐US Marine Biodiversity GroupUniversidad de AlcaláAlcalá de HenaresSpain
- Departamento de Biología (Zoología)Universidad Autónoma de MadridFacultad de CienciasMadridSpain
| | - Carlos Leiva
- Department of Life SciencesThe Natural History MuseumLondonUK
- Department of Genetics, Microbiology and StatisticsFaculty of BiologyUniversity of BarcelonaBarcelonaSpain
| | - Kathrin Busch
- GEOMAR Helmholtz Centre for Ocean Research KielResearch Unit Marine SymbiosesKielGermany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research KielResearch Unit Marine SymbiosesKielGermany
| | - Ana Riesgo
- Department of Life SciencesThe Natural History MuseumLondonUK
- Department of Biodiversity and Evolutionary BiologyMuseo Nacional de Ciencias Naturales de Madrid (CSIC)MadridSpain
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39
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Griffiths SM, Butler MJ, Behringer DC, Pérez T, Preziosi RF. Oceanographic features and limited dispersal shape the population genetic structure of the vase sponge Ircinia campana in the Greater Caribbean. Heredity (Edinb) 2020; 126:63-76. [PMID: 32699391 PMCID: PMC7852562 DOI: 10.1038/s41437-020-0344-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 07/13/2020] [Accepted: 07/13/2020] [Indexed: 11/10/2022] Open
Abstract
Understanding population genetic structure can help us to infer dispersal patterns, predict population resilience and design effective management strategies. For sessile species with limited dispersal, this is especially pertinent because genetic diversity and connectivity are key aspects of their resilience to environmental stressors. Here, we describe the population structure of Ircinia campana, a common Caribbean sponge subject to mass mortalities and disease. Microsatellites were used to genotype 440 individuals from 19 sites throughout the Greater Caribbean. We found strong genetic structure across the region, and significant isolation by distance across the Lesser Antilles, highlighting the influence of limited larval dispersal. We also observed spatial genetic structure patterns congruent with oceanography. This includes evidence of connectivity between sponges in the Florida Keys and the southeast coast of the United States (>700 km away) where the oceanographic environment is dominated by the strong Florida Current. Conversely, the population in southern Belize was strongly differentiated from all other sites, consistent with the presence of dispersal-limiting oceanographic features, including the Gulf of Honduras gyre. At smaller spatial scales (<100 km), sites showed heterogeneous patterns of low-level but significant genetic differentiation (chaotic genetic patchiness), indicative of temporal variability in recruitment or local selective pressures. Genetic diversity was similar across sites, but there was evidence of a genetic bottleneck at one site in Florida where past mass mortalities have occurred. These findings underscore the relationship between regional oceanography and weak larval dispersal in explaining population genetic patterns, and could inform conservation management of the species.
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Affiliation(s)
- Sarah M Griffiths
- Ecology and Environment Research Centre, Manchester Metropolitan University, Manchester, UK.
| | - Mark J Butler
- Department of Biological Sciences, Institute of Environment, Florida International University, North Miami, FL, USA
| | - Donald C Behringer
- Fisheries and Aquatic Sciences, University of Florida, Gainesville, FL, USA.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Thierry Pérez
- Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale, Aix Marseille Université, Marseille, France
| | - Richard F Preziosi
- Ecology and Environment Research Centre, Manchester Metropolitan University, Manchester, UK
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40
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Prabhu VR, Wasimuddin, Kamalakkannan R, Arjun MS, Nagarajan M. Consequences of Domestication on Gut Microbiome: A Comparative Study Between Wild Gaur and Domestic Mithun. Front Microbiol 2020; 11:133. [PMID: 32158434 PMCID: PMC7051944 DOI: 10.3389/fmicb.2020.00133] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
Although the gut microbiome benefits the host in several ways, how anthropogenic forces impact the gut microbiome of mammals is not yet completely known. Recent studies have noted reduced gut microbiome diversity in captive mammals due to changes in diet and living environment. However, no studies have been carried out to understand how the gut microbiome of wild mammals responds to domestication. We analyzed the gut microbiome of wild and captive gaur and domestic mithun (domestic form of gaur) to understand whether the gut microbiome exhibits sequential changes from wild to captivity and after domestication. Both captive and domestic populations were characterized by reduced microbial diversity and abundance as compared to their wild counterparts. Notably, two beneficial bacterial families, Ruminococcaceae and Lachnospiraceae, which are known to play vital roles in herbivores' digestion, exhibited lower abundance in captive and domestic populations. Consequently, the predicted bacterial functional pathways especially related to metabolism and immune system showed lower abundance in captive and domestic populations compared to wild population. Therefore, we suggest that domestication can impact the gut microbiome more severely than captivity, which might lead to adverse effects on host health and fitness. However, further investigations are required across a wide range of domesticates in order to understand the general trend of microbiome shifts in domestic animals.
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Affiliation(s)
- Vandana R. Prabhu
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Wasimuddin
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Ranganathan Kamalakkannan
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Moolamkudy Suresh Arjun
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Muniyandi Nagarajan
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
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41
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Chung SH, Parker BJ, Blow F, Brisson JA, Douglas AE. Host and symbiont genetic determinants of nutritional phenotype in a natural population of the pea aphid. Mol Ecol 2020; 29:848-858. [PMID: 31945243 DOI: 10.1111/mec.15355] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/20/2019] [Accepted: 01/08/2020] [Indexed: 12/17/2022]
Abstract
A defining feature of the nutritional ecology of plant sap-feeding insects is that the dietary deficit of essential amino acids (EAAs) in plant sap is supplemented by EAA-provisioning microbial symbionts in the insect. Here, we demonstrated substantial variation in the nutritional phenotype of 208 genotypes of the pea aphid Acyrthosiphon pisum collected from a natural population. Specifically, the genotypes varied in performance (larval growth rates) on four test diets lacking the EAAs arginine, histidine and methionine or aromatic EAAs (phenylalanine and tryptophan), relative to the diet containing all EAAs. These data indicate that EAA supply from the symbiotic bacteria Buchnera can meet total aphid nutritional demand for only a subset of the EAA/aphid genotype combinations. We then correlated single nucleotide polymorphisms (SNPs) identified in the aphid and Buchnera genomes by reduced genome sequencing against aphid performance for each EAA deletion diet. This yielded significant associations between performance on the histidine-free diet and Buchnera SNPs, including metabolism genes predicted to influence histidine biosynthesis. Aphid genetic correlates of performance were obtained for all four deletion diets, with associations on the arginine-free diet and aromatic-free diets dominated by genes functioning in the regulation of metabolic and cellular processes. The specific aphid genes associated with performance on different EAA deletion diets are largely nonoverlapping, indicating some independence in the regulatory circuits determining aphid phenotype for the different EAAs. This study demonstrates how variation in the phenotype of associations collected from natural populations can be applied to elucidate the genetic basis of ecologically important traits in systems intractable to traditional forward/reverse genetic techniques.
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Affiliation(s)
- Seung Ho Chung
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | | | - Frances Blow
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | | | - Angela E Douglas
- Department of Entomology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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42
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Easson CG, Chaves-Fonnegra A, Thacker RW, Lopez JV. Host population genetics and biogeography structure the microbiome of the sponge Cliona delitrix. Ecol Evol 2020; 10:2007-2020. [PMID: 32128133 PMCID: PMC7042757 DOI: 10.1002/ece3.6033] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/13/2022] Open
Abstract
Sponges occur across diverse marine biomes and host internal microbial communities that can provide critical ecological functions. While strong patterns of host specificity have been observed consistently in sponge microbiomes, the precise ecological relationships between hosts and their symbiotic microbial communities remain to be fully delineated. In the current study, we investigate the relative roles of host population genetics and biogeography in structuring the microbial communities hosted by the excavating sponge Cliona delitrix. A total of 53 samples, previously used to demarcate the population genetic structure of C. delitrix, were selected from two locations in the Caribbean Sea and from eight locations across the reefs of Florida and the Bahamas. Microbial community diversity and composition were measured using Illumina-based high-throughput sequencing of the 16S rRNA V4 region and related to host population structure and geographic distribution. Most operational taxonomic units (OTUs) specific to Cliona delitrix microbiomes were rare, while other OTUs were shared with congeneric hosts. Across a large regional scale (>1,000 km), geographic distance was associated with considerable variability of the sponge microbiome, suggesting a distance-decay relationship, but little impact over smaller spatial scales (<300 km) was observed. Host population structure had a moderate effect on the structure of these microbial communities, regardless of geographic distance. These results support the interplay between geographic, environmental, and host factors as forces determining the community structure of microbiomes associated with C. delitrix. Moreover, these data suggest that the mechanisms of host regulation can be observed at the population genetic scale, prior to the onset of speciation.
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Affiliation(s)
- Cole G. Easson
- Department of BiologyMiddle Tennessee State UniversityMurfreesboroTN
- Halmos College of Natural Sciences and OceanographyNova Southeastern UniversityDania BeachFL
| | - Andia Chaves-Fonnegra
- Harriet L. Wilkes Honors CollegeHarbor Branch Oceanographic InstituteFlorida Atlantic UniversityFort PierceFL
| | - Robert W. Thacker
- Department of Ecology and EvolutionStony Brook UniversityStony BrookNY
| | - Jose V. Lopez
- Halmos College of Natural Sciences and OceanographyNova Southeastern UniversityDania BeachFL
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Griffiths SM, Antwis RE, Lenzi L, Lucaci A, Behringer DC, Butler MJ, Preziosi RF. Host genetics and geography influence microbiome composition in the sponge Ircinia campana. J Anim Ecol 2019; 88:1684-1695. [PMID: 31325164 PMCID: PMC6899969 DOI: 10.1111/1365-2656.13065] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/09/2019] [Indexed: 12/22/2022]
Abstract
Marine sponges are hosts to large, diverse communities of microorganisms. These microbiomes are distinct among sponge species and from seawater bacterial communities, indicating a key role of host identity in shaping its resident microbial community. However, the factors governing intraspecific microbiome variability are underexplored and may shed light on the evolutionary and ecological relationships between host and microbiome. Here, we examined the influence of genetic variation and geographic location on the composition of the Ircinia campana microbiome. We developed new microsatellite markers to genotype I. campana from two locations in the Florida Keys, USA, and characterized their microbiomes using V4 16S rRNA amplicon sequencing. We show that microbial community composition and diversity is influenced by host genotype, with more genetically similar sponges hosting more similar microbial communities. We also found that although I. campana was not genetically differentiated between sites, microbiome composition differed by location. Our results demonstrate that both host genetics and geography influence the composition of the sponge microbiome. Host genotypic influence on microbiome composition may be due to stable vertical transmission of the microbial community from parent to offspring, making microbiomes more similar by descent. Alternatively, sponge genotypic variation may reflect variation in functional traits that influence the acquisition of environmental microbes. This study reveals drivers of microbiome variation within and among locations, and shows the importance of intraspecific variability in mediating eco-evolutionary dynamics of host-associated microbiomes.
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Affiliation(s)
- Sarah M. Griffiths
- Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
| | - Rachael E. Antwis
- School of Environment and Life SciencesUniversity of SalfordSalfordUK
| | - Luca Lenzi
- Centre for Genomic Research, Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Anita Lucaci
- Centre for Genomic Research, Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Donald C. Behringer
- Fisheries and Aquatic SciencesUniversity of FloridaGainesvilleFLUSA
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFLUSA
| | - Mark J. Butler
- Department of Biological SciencesOld Dominion UniversityNorfolkVAUSA
| | - Richard F. Preziosi
- Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
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