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Paix B, van der Valk E, de Voogd NJ. Dynamics, diversity, and roles of bacterial transmission modes during the first asexual life stages of the freshwater sponge Spongilla lacustris. ENVIRONMENTAL MICROBIOME 2024; 19:37. [PMID: 38851755 PMCID: PMC11162577 DOI: 10.1186/s40793-024-00580-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND Sponge-associated bacteria play important roles in the physiology of their host, whose recruitment processes are crucial to maintain symbiotic associations. However, the acquisition of bacterial communities within freshwater sponges is still under explored. Spongilla lacustris is a model sponge widely distributed in European rivers and lakes, producing dormant cysts (named gemmules) for their asexual reproduction, before winter. Through an in vitro experiment, this study aims to describe the dynamics of bacterial communities and their transmission modes following the hatching of these gemmules. RESULTS An overall change of bacterial β-diversity was observed through the ontology of the juvenile sponges. These temporal differences were potentially linked, first to the osculum acquisition and the development of a canal system, and then, the increasing colonization of the Chlorella-like photosymbionts. Gemmules hatching with a sterilized surface were found to have a more dispersed and less diverse microbiome, revealing the importance of gemmule epibacteria for the whole holobiont stability. These epibacteria were suggested to be vertically transmitted from the maternal tissues to the gemmule surface. Vertical transmission through the incorporation of bacterial communities inside of the gemmule, was also found as a dominant transmission mode, especially with the nitrogen fixers Terasakiellaceae. Finally, we showed that almost no ASVs were shared between the free-living community and the juveniles, suggesting that horizontal recruitment is unlikely to happen during the first stages of development. However, the free-living bacteria filtered are probably used as a source of nutrients, allowing an enrichment of copiotrophic bacteria already present within its microbiome. CONCLUSIONS This study brings new insight for a better understanding of the microbiome acquisition during the first stages of freshwater sponge development. We showed the importance of epibacterial communities on gemmules for the whole holobiont stability, and demonstrated the near absence of recruitment of free-living bacteria during the first stages.
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Affiliation(s)
- Benoit Paix
- Naturalis Biodiversity Center, Leiden, The Netherlands.
- UMR CARRTEL, INRAE - Université Savoie Mont-Blanc, Thonon-les-Bains, France.
| | - Elodie van der Valk
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Biology (IBL), Leiden University, PO Box 9505, Leiden, 2333BE, The Netherlands
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, Leiden, The Netherlands.
- Institute of Biology (IBL), Leiden University, PO Box 9505, Leiden, 2333BE, The Netherlands.
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2
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Mazzella V, Dell'Anno A, Etxebarría N, González-Gaya B, Nuzzo G, Fontana A, Núñez-Pons L. High microbiome and metabolome diversification in coexisting sponges with different bio-ecological traits. Commun Biol 2024; 7:422. [PMID: 38589605 PMCID: PMC11001883 DOI: 10.1038/s42003-024-06109-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Marine Porifera host diverse microbial communities, which influence host metabolism and fitness. However, functional relationships between sponge microbiomes and metabolic signatures are poorly understood. We integrate microbiome characterization, metabolomics and microbial predicted functions of four coexisting Mediterranean sponges -Petrosia ficiformis, Chondrosia reniformis, Crambe crambe and Chondrilla nucula. Microscopy observations reveal anatomical differences in microbial densities. Microbiomes exhibit strong species-specific trends. C. crambe shares many rare amplicon sequence variants (ASV) with the surrounding seawater. This suggests important inputs of microbial diversity acquired by selective horizontal acquisition. Phylum Cyanobacteria is mainly represented in C. nucula and C. crambe. According to putative functions, the microbiome of P. ficiformis and C. reniformis are functionally heterotrophic, while C. crambe and C. nucula are autotrophic. The four species display distinct metabolic profiles at single compound level. However, at molecular class level they share a "core metabolome". Concurrently, we find global microbiome-metabolome association when considering all four sponge species. Within each species still, sets of microbe/metabolites are identified driving multi-omics congruence. Our findings suggest that diverse microbial players and metabolic profiles may promote niche diversification, but also, analogous phenotypic patterns of "symbiont evolutionary convergence" in sponge assemblages where holobionts co-exist in the same area.
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Affiliation(s)
- Valerio Mazzella
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Ischia Marine Centre, 80077, Ischia, Naples, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy
| | - Antonio Dell'Anno
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy.
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Néstor Etxebarría
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Belén González-Gaya
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Genoveffa Nuzzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
| | - Angelo Fontana
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
- Department of Biology, University of Naples Federico II, Via Cinthia-Bld. 7, 80126, Napoli, Italy
| | - Laura Núñez-Pons
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy.
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
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Efremova J, Mazzella V, Mirasole A, Teixidó N, Núñez-Pons L. Divergent morphological and microbiome strategies of two neighbor sponges to cope with low pH in Mediterranean CO 2 vents. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170171. [PMID: 38246375 DOI: 10.1016/j.scitotenv.2024.170171] [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: 09/06/2023] [Revised: 12/23/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
Ocean Acidification (OA) profoundly impacts marine biochemistry, resulting in a net loss of biodiversity. Porifera are often forecasted as winner taxa, yet the strategies to cope with OA can vary and may generate diverse fitness status. In this study, microbial shifts based on the V3-V4 16S rRNA gene marker were compared across neighboring Chondrosia reniformis sponges with high microbial abundance (HMA), and Spirastrella cunctatrix with low microbial abundance (LMA) microbiomes. Sponge holobionts co-occurred in a CO2 vent system with low pH (pHT ~ 7.65), and a control site with Ambient pH (pHT ~ 8.05) off Ischia Island, representing natural analogues to study future OA, and species' responses in the face of global environmental change. Microbial diversity and composition varied in both species across sites, yet at different levels. Increased numbers of core taxa were detected in S. cunctatrix, and a more diverse and flexible core microbiome was reported in C. reniformis under OA. Vent S. cunctatrix showed morphological impairment, along with signs of putative stress-induced dysbiosis, manifested by: 1) increases in alpha diversity, 2) shifts from sponge related microbes towards seawater microbes, and 3) high dysbiosis scores. Chondrosia reniformis in lieu, showed no morphological variation, low dysbiosis scores, and experienced a reduction in alpha diversity and less number of core taxa in vent specimens. Therefore, C. reniformis is hypothesized to maintain an state of normobiosis and acclimatize to OA, thanks to a more diverse, and likely metabolically versatile microbiome. A consortium of differentially abundant microbes was identified associated to either vent or control sponges, and chiefly related to carbon, nitrogen and sulfur-metabolisms for nutrient cycling and vitamin production, as well as probiotic symbionts in C. reniformis. Diversified symbiont associates supporting functional convergence could be the key behind resilience towards OA, yet specific acclimatization traits should be further investigated.
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Affiliation(s)
- Jana Efremova
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy.
| | - Valerio Mazzella
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy.
| | - Alice Mirasole
- Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy.
| | - Núria Teixidó
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy; Laboratoire d'Océanographie de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-mer, France.
| | - Laura Núñez-Pons
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy.
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4
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Turon M, Ford M, Maldonado M, Sitjà C, Riesgo A, Díez-Vives C. Microbiome changes through the ontogeny of the marine sponge Crambe crambe. ENVIRONMENTAL MICROBIOME 2024; 19:15. [PMID: 38468324 DOI: 10.1186/s40793-024-00556-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/21/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND Poriferans (sponges) are highly adaptable organisms that can thrive in diverse marine and freshwater environments due, in part, to their close associations with internal microbial communities. This sponge microbiome can be acquired from the surrounding environment (horizontal acquisition) or obtained from the parents during the reproductive process through a variety of mechanisms (vertical transfer), typically resulting in the presence of symbiotic microbes throughout all stages of sponge development. How and to what extent the different components of the microbiome are transferred to the developmental stages remain poorly understood. Here, we investigated the microbiome composition of a common, low-microbial-abundance, Atlantic-Mediterranean sponge, Crambe crambe, throughout its ontogeny, including adult individuals, brooded larvae, lecithotrophic free-swimming larvae, newly settled juveniles still lacking osculum, and juveniles with a functional osculum for filter feeding. RESULTS Using 16S rRNA gene analysis, we detected distinct microbiome compositions in each ontogenetic stage, with variations in composition, relative abundance, and diversity of microbial species. However, a particular dominant symbiont, Candidatus Beroebacter blanensis, previously described as the main symbiont of C. crambe, consistently occurred throughout all stages, an omnipresence that suggests vertical transmission from parents to offspring. This symbiont fluctuated in relative abundance across developmental stages, with pronounced prevalence in lecithotrophic stages. A major shift in microbial composition occurred as new settlers completed osculum formation and acquired filter-feeding capacity. Candidatus Beroebacter blanensis decreased significatively at this point. Microbial diversity peaked in filter-feeding stages, contrasting with the lower diversity of lecithotrophic stages. Furthermore, individual specific transmission patterns were detected, with greater microbial similarity between larvae and their respective parents compared to non-parental conspecifics. CONCLUSIONS These findings suggest a putative vertical transmission of the dominant symbiont, which could provide some metabolic advantage to non-filtering developmental stages of C. crambe. The increase in microbiome diversity with the onset of filter-feeding stages likely reflects enhanced interaction with environmental microbes, facilitating horizontal transmission. Conversely, lower microbiome diversity in lecithotrophic stages, prior to filter feeding, suggests incomplete symbiont transfer or potential symbiont digestion. This research provides novel information on the dynamics of the microbiome through sponge ontogeny, on the strategies for symbiont acquisition at each ontogenetic stage, and on the potential importance of symbionts during larval development.
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Affiliation(s)
- Marta Turon
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), c/José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Madeline Ford
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Manuel Maldonado
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), c/Accés a la Cala St. Francesc, 14, 17300, Blanes, Spain
| | - Cèlia Sitjà
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), c/Accés a la Cala St. Francesc, 14, 17300, Blanes, Spain
| | - Ana Riesgo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), c/José Gutiérrez Abascal 2, 28006, Madrid, Spain.
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
| | - Cristina Díez-Vives
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
- Department of Systems Biology, Centro Nacional de Biotecnología, c/Darwin, 3, 28049, Madrid, Spain.
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5
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Zhang B, Jia C, Li M, Wang K, Chen J, Zhao J. Multiomics integration for the function of bacterial outer membrane vesicles in the larval settlement of marine sponges. Front Microbiol 2024; 15:1268813. [PMID: 38468855 PMCID: PMC10925772 DOI: 10.3389/fmicb.2024.1268813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/26/2024] [Indexed: 03/13/2024] Open
Abstract
Bacterial outer membrane vesicles (OMVs) contain a variety of chemical compounds and play significant roles in maintaining symbiotic relationships in a changing ocean, but little is known about their function, particularly in sponge larval development. During the growth of sponge Tedania sp., OMVs from Bacteroidetes species significantly promoted larval settlement, and Tenacibaculum mesophilum SP-7-OMVs were selected as a representative strain for further investigation. According to OMVs metabolomics, larval settlement might be connected to organic acids and derivatives. The multiomics analysis of the T. mesophilum genome, SP-7-OMVs metabolome, and larval transcriptome revealed 47 shared KEGG pathways. Among the number of candidate metabolites, arginine was chosen for its greater ability to increase the settlement rate and its role as the principal substrate for nitric oxide (NO) synthesis of sponge larvae. In summary, these results demonstrated that sponge-associated bacteria might utilize OMVs and their cargo to support host development and make up for host metabolic pathway deficiencies. This study enhances our fundamental knowledge of OMVs in interactions between metazoan hosts and microorganisms that are crucial in the coevolution of marine ecosystems and the complex marine environment.
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Affiliation(s)
- Beibei Zhang
- College of Ocean and Earth Sciences, Xiamen University, Xaimen, Fujian, China
| | - Chenzheng Jia
- College of Ocean and Earth Sciences, Xiamen University, Xaimen, Fujian, China
| | - Mingyu Li
- College of Ocean and Earth Sciences, Xiamen University, Xaimen, Fujian, China
| | - Kai Wang
- College of Ocean and Earth Sciences, Xiamen University, Xaimen, Fujian, China
| | - Jun Chen
- College of Ocean and Earth Sciences, Xiamen University, Xaimen, Fujian, China
| | - Jing Zhao
- College of Ocean and Earth Sciences, Xiamen University, Xaimen, Fujian, China
- Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration (USER), Xiamen University, Xiamen, Fujian, China
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6
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Syukur S, Richmond J, Majzoub ME, Nappi J, Egan S, Thomas T. Not all parents are the same: Diverse strategies of symbiont transmission in seaweeds. Environ Microbiol 2024; 26:e16564. [PMID: 38151764 DOI: 10.1111/1462-2920.16564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/11/2023] [Indexed: 12/29/2023]
Abstract
Different marine seaweed species have been shown to harbour specific bacterial communities, however, the extent to which vertical symbiont transmission from parents to offspring contributes to host-specificity is unclear. Here we use fluorescence and electron microscopy as well as 16S rRNA gene-based community analysis to investigate symbiont transmission in members of the three major seaweed groups (green Chlorophyta, red Rhodophyta and brown Phaeophyceae). We found seaweeds employ diverse strategies to transfer symbionts to their progeny. For instance, the green Ulva australis does not appear to have the capacity for vertical transmission. In contrast, the brown Phyllospora comosa adopts a non-selective vertical transmission. The red Delisea pulchra demonstrates weak selectivity in symbiont transmission, while the brown Hormosira banksii exhibits a strongly selective symbiont transfer. Mucilage on the gametes appears to facilitate vertical transmission and transferred bacteria have predicted properties that could support early development of the seaweeds. Previous meta-analysis has indicated that vertical transmission is rare in aquatic compared to terrestrial environments, however, our results contribute to the growing evidence that this might not be the case and that instead vertical transmission with various degrees of symbiont selection occurs in the ecologically important group of seaweeds.
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Affiliation(s)
- Syukur Syukur
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Kensington, Australia
| | - Joanna Richmond
- Electron Microscope Unit, Mark Wainwright Analytical Centre, UNSW Sydney, Kensington, Australia
| | - Marwan E Majzoub
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Kensington, Australia
| | - Jadranka Nappi
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Kensington, Australia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Kensington, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Kensington, Australia
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7
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O'Brien PA, Tan S, Frade PR, Robbins SJ, Engelberts JP, Bell SC, Vanwonterghem I, Miller DJ, Webster NS, Zhang G, Bourne DG. Validation of key sponge symbiont pathways using genome-centric metatranscriptomics. Environ Microbiol 2023; 25:3207-3224. [PMID: 37732569 DOI: 10.1111/1462-2920.16509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023]
Abstract
The sponge microbiome underpins host function through provision and recycling of essential nutrients in a nutrient poor environment. Genomic data suggest that carbohydrate degradation, carbon fixation, nitrogen metabolism, sulphur metabolism and supplementation of B-vitamins are central microbial functions. However, validation beyond the genomic potential of sponge symbiont pathways is rarely explored. To evaluate metagenomic predictions, we sequenced the metagenomes and metatranscriptomes of three common coral reef sponges: Ircinia ramosa, Ircinia microconulosa and Phyllospongia foliascens. Multiple carbohydrate active enzymes were expressed by Poribacteria, Bacteroidota and Cyanobacteria symbionts, suggesting these lineages have a central role in assimilating dissolved organic matter. Expression of entire pathways for carbon fixation and multiple sulphur compound transformations were observed in all sponges. Gene expression for anaerobic nitrogen metabolism (denitrification and nitrate reduction) were more common than aerobic metabolism (nitrification), where only the I. ramosa microbiome expressed the nitrification pathway. Finally, while expression of the biosynthetic pathways for B-vitamins was common, the expression of additional transporter genes was far more limited. Overall, we highlight consistencies and disparities between metagenomic and metatranscriptomic results when inferring microbial activity, while uncovering new microbial taxa that contribute to the health of their sponge host via nutrient exchange.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Shangjin Tan
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | | | - Steven J Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - J Pamela Engelberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
- Centre for Microbiome Research, Translational Research Institute, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Sara C Bell
- Australian Institute of Marine Science, Townsville, Queensland, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
- Australian Antarctic Division, Department of Climate Change, Energy, Environment and Water, Kingston, Tasmania, Australia
| | - Guojie Zhang
- Centre for Evolutionary & Organismal Biology and Women's Hospital, Zhejiang University, School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Townsville, Queensland, Australia
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8
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Sinotte VM, Renelies-Hamilton J, Andreu-Sánchez S, Vasseur-Cognet M, Poulsen M. Selective enrichment of founding reproductive microbiomes allows extensive vertical transmission in a fungus-farming termite. Proc Biol Sci 2023; 290:20231559. [PMID: 37848067 PMCID: PMC10581767 DOI: 10.1098/rspb.2023.1559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/09/2023] [Indexed: 10/19/2023] Open
Abstract
Mutualistic coevolution can be mediated by vertical transmission of symbionts between host generations. Termites host complex gut bacterial communities with evolutionary histories indicative of mixed-mode transmission. Here, we document that vertical transmission of gut bacterial strains is congruent across parent to offspring colonies in four pedigrees of the fungus-farming termite Macrotermes natalensis. We show that 44% of the offspring colony microbiome, including more than 80 bacterial genera and pedigree-specific strains, are consistently inherited. We go on to demonstrate that this is achieved because colony-founding reproductives are selectively enriched with a set of non-random, environmentally sensitive and termite-specific gut microbes from their colonies of origin. These symbionts transfer to offspring colony workers with high fidelity, after which priority effects appear to influence the composition of the establishing microbiome. Termite reproductives thus secure transmission of complex communities of specific, co-evolved microbes that are critical to their offspring colonies. Extensive yet imperfect inheritance implies that the maturing colony benefits from acquiring environmental microbes to complement combinations of termite, fungus and vertically transmitted microbes; a mode of transmission that is emerging as a prevailing strategy for hosts to assemble complex adaptive microbiomes.
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Affiliation(s)
- Veronica M. Sinotte
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen East, Denmark
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Justinn Renelies-Hamilton
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen East, Denmark
| | - Sergio Andreu-Sánchez
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen East, Denmark
- Department of Paediatrics, University Medical Centre Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Mireille Vasseur-Cognet
- UMR IRD 242, UPEC, CNRS 7618, UPMC 113, INRAe 1392, Paris 7 113, Institute of Ecology and Environmental Sciences of Paris, Bondy, France
- Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen East, Denmark
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9
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Bruijning M, Ayroles JF, Henry LP, Koskella B, Meyer KM, Metcalf CJE. Relative abundance data can misrepresent heritability of the microbiome. MICROBIOME 2023; 11:222. [PMID: 37814275 PMCID: PMC10561453 DOI: 10.1186/s40168-023-01669-w] [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: 05/31/2022] [Accepted: 09/13/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND Host genetics can shape microbiome composition, but to what extent it does, remains unclear. Like any other complex trait, this important question can be addressed by estimating the heritability (h2) of the microbiome-the proportion of variance in the abundance in each taxon that is attributable to host genetic variation. However, unlike most complex traits, microbiome heritability is typically based on relative abundance data, where taxon-specific abundances are expressed as the proportion of the total microbial abundance in a sample. RESULTS We derived an analytical approximation for the heritability that one obtains when using such relative, and not absolute, abundances, based on an underlying quantitative genetic model for absolute abundances. Based on this, we uncovered three problems that can arise when using relative abundances to estimate microbiome heritability: (1) the interdependency between taxa can lead to imprecise heritability estimates. This problem is most apparent for dominant taxa. (2) Large sample size leads to high false discovery rates. With enough statistical power, the result is a strong overestimation of the number of heritable taxa in a community. (3) Microbial co-abundances lead to biased heritability estimates. CONCLUSIONS We discuss several potential solutions for advancing the field, focusing on technical and statistical developments, and conclude that caution must be taken when interpreting heritability estimates and comparing values across studies. Video Abstract.
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Affiliation(s)
- Marjolein Bruijning
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE, Amsterdam, The Netherlands.
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA.
| | - Julien F Ayroles
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ, 08544, USA
| | - Lucas P Henry
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ, 08544, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York City, 10003, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Kyle M Meyer
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
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10
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Zhang XY, Khakisahneh S, Liu W, Zhang X, Zhai W, Cheng J, Speakman JR, Wang DH. Phylogenetic signal in gut microbial community rather than in rodent metabolic traits. Natl Sci Rev 2023; 10:nwad209. [PMID: 37928774 PMCID: PMC10625476 DOI: 10.1093/nsr/nwad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 07/10/2023] [Accepted: 07/19/2023] [Indexed: 11/07/2023] Open
Abstract
Host phylogeny and environment have all been implicated in shaping the gut microbiota and host metabolic traits of mammals. However, few studies have evaluated phylogeny-associated microbial assembly and host metabolic plasticity concurrently, and their relationships on both short-term and evolutionary timescales. We report that the branching order of a gut microbial dendrogram was nearly congruent with phylogenetic relationships of seven rodent species, and this pattern of phylosymbiosis was intact after diverse laboratory manipulations. Laboratory rearing, diet or air temperature (Ta) acclimation induced alterations in gut microbial communities, but could not override host phylogeny in shaping microbial community assembly. A simulative heatwave reduced core microbiota diversity by 26% in these species, and led to an unmatched relationship between the microbiota and host metabolic phenotypes in desert species. Moreover, the similarity of metabolic traits across species at different Tas was not correlated with phylogenetic distance. These data demonstrated that the gut microbial assembly showed strong concordance with host phylogeny and may be shaped by environmental variables, whereas host metabolic traits did not seem to be linked with phylogeny.
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Affiliation(s)
- Xue-Ying Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Saeid Khakisahneh
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinyi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Animal Evolution and Genetics, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - John R Speakman
- Shenzhen Key Laboratory of Metabolic Health, Center for Energy Metabolism and Reproduction, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB39 2PN, UK
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - De-Hua Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, Shandong University, Qingdao 266237, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Steffen K, Proux-Wéra E, Soler L, Churcher A, Sundh J, Cárdenas P. Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae). G3 (BETHESDA, MD.) 2023; 13:jkad192. [PMID: 37619978 PMCID: PMC10542158 DOI: 10.1093/g3journal/jkad192] [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: 02/22/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/26/2023]
Abstract
Sponges are among the earliest branching extant animals. As such, genetic data from this group are valuable for understanding the evolution of various traits and processes in other animals. However, like many marine organisms, they are notoriously difficult to sequence, and hence, genomic data are scarce. Here, we present the draft genome assembly for the North Atlantic deep-sea high microbial abundance species Geodia barretti Bowerbank 1858, from a single individual collected on the West Coast of Sweden. The nuclear genome assembly has 4,535 scaffolds, an N50 of 48,447 bp and a total length of 144 Mb; the mitochondrial genome is 17,996 bp long. BUSCO completeness was 71.5%. The genome was annotated using a combination of ab initio and evidence-based methods finding 31,884 protein-coding genes.
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Affiliation(s)
- Karin Steffen
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala 751 24, Sweden
| | - Estelle Proux-Wéra
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna SE-17121, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala University, Uppsala 752 37, Sweden
| | - Allison Churcher
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Umeå University, Umeå 901 87, Sweden
| | - John Sundh
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna SE-17121, Sweden
| | - Paco Cárdenas
- Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, Uppsala 751 24, Sweden
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12
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Hyde J, Brackney DE, Steven B. Three species of axenic mosquito larvae recruit a shared core of bacteria in a common garden experiment. Appl Environ Microbiol 2023; 89:e0077823. [PMID: 37681948 PMCID: PMC10537770 DOI: 10.1128/aem.00778-23] [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: 05/08/2023] [Accepted: 07/05/2023] [Indexed: 09/09/2023] Open
Abstract
In this study, we describe the generation of two new species of axenic mosquito, Aedes albopictus and Aedes triseriatus. Along with Aedes aegypti, axenic larvae of these three species were exposed to an environmental water source to document the assembly of the microbiome in a common garden experiment. Additionally, the larvae were reared either individually or combinatorially with the other species to characterize the effects of co-rearing on the composition of the microbiome. We found that the microbiome of the larvae was composed of a relatively low-diversity collection of bacteria from the colonizing water. The abundance of bacteria in the water was a poor predictor of their abundance in the larvae, suggesting the larval microbiome is made up of a subset of relatively rare aquatic bacteria. We found 11 bacterial 16S rRNA gene amplicon sequence variants (ASVs) that were conserved among ≥90% of the mosquitoes sampled, including 2 found in 100% of the larvae, pointing to a conserved core of bacteria capable of colonizing all three species of mosquito. Yet, the abundance of these ASVs varied widely between larvae, suggesting individuals harbored largely unique microbiome structures, even if they overlapped in membership. Finally, larvae reared in a tripartite mix of the host-species consistently showed a convergence in the structure of their microbiome, indicating that multi-species interactions between hosts potentially lead to shifts in the composition of their respective microbiomes. IMPORTANCE This study is the first report of the axenic (free of external microbes) rearing of two species of mosquito, Aedes albopictus and Aedes triseriatus. Our previous report of axenic Aedes aegypti brings the number of axenic species to three. We designed a method to perform a common garden experiment to characterize the bacteria the three species of axenic larvae assemble from their surroundings. Furthermore, species could be reared in isolation or in multi-species combinations to assess how host-species interactions influence the composition of the microbiome. We found all three species recruited a common core of bacteria from their rearing water, with a large contingent of rare and sporadically detected bacteria. Finally, we also show that co-rearing of mosquito larvae leads to a coalescence in the composition of their microbiome, indicating that host-species interactions potentially influence the composition of the microbiome.
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Affiliation(s)
- Josephine Hyde
- Department of Environmental Science and Forestry, Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Doug E. Brackney
- Department of Entomology, Center for Vector Biology and Zoonotic Diseases, Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
| | - Blaire Steven
- Department of Environmental Science and Forestry, Connecticut Agricultural Experiment Station, New Haven, Connecticut, USA
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13
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Garritano AN, Majzoub ME, Ribeiro B, Damasceno T, Modolon F, Messias C, Vilela C, Duarte G, Hill L, Peixoto R, Thomas T. Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae. THE ISME JOURNAL 2023; 17:1517-1519. [PMID: 37258653 PMCID: PMC10432484 DOI: 10.1038/s41396-023-01439-4] [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: 02/12/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/02/2023]
Abstract
Sponges thrive in the deep, dark and nutrient-depleted ocean and may rely on microbial symbionts for carbon acquisition and energy generation. However, these symbiotic relationships remain largely unexplored. In this study, we analyze the microbiome of deep-sea sponges and show that ammonia-oxidizing archaea (AOA) of the family Nitrosopumilaceae make up at least 75% of the microbial communities of the sponges Aphrocallistes sp., Farrea sp. and Paratimea sp.. Given the known autotrophic metabolism of AOAs, this implies that these sponge holobionts can have the capacity for primary production in the deep-sea. We also show that specific AOA lineages are highly specific towards their hosts, hinting towards an unprecedent vertical transmission of these symbionts in deep-sea sponges. Our results show that the ecology and evolution of symbiotic relationships in deep-sea sponge is distinct from that of their shallow-water counterparts.
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Affiliation(s)
- Alessandro N Garritano
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, 2052, Australia
| | - Marwan E Majzoub
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, 2052, Australia
| | - Bárbara Ribeiro
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Taissa Damasceno
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Microbiologia Paulo de Goes, LEMM Laboratory, Rio de Janeiro, Brazil
| | - Fluvio Modolon
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Microbiologia Paulo de Goes, LEMM Laboratory, Rio de Janeiro, Brazil
| | - Camila Messias
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Microbiologia Paulo de Goes, LEMM Laboratory, Rio de Janeiro, Brazil
| | - Caren Vilela
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Microbiologia Paulo de Goes, LEMM Laboratory, Rio de Janeiro, Brazil
| | - Gustavo Duarte
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Microbiologia Paulo de Goes, LEMM Laboratory, Rio de Janeiro, Brazil
| | - Lilian Hill
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Departamento de Microbiologia Paulo de Goes, LEMM Laboratory, Rio de Janeiro, Brazil
| | - Raquel Peixoto
- King Abdullah University of Science and Technology, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, 2052, Australia.
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14
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ALAKUŞ TB. Classification of Microbes with Recurrent Neural Networks. FIRAT ÜNIVERSITESI MÜHENDISLIK BILIMLERI DERGISI 2023. [DOI: 10.35234/fumbd.1302903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Mikroplar insan vücudunun hem içinde hem de dışında yaşayan ve hemen hemen her yerde bulunan tek hücreli küçük canlılardır. Zararlı olabileceği gibi zararı olmayan mikroplarda bulunmaktadır. Bu yüzden mikroplar ekolojik dengenin sağlanmasında büyük bir rol üstlenmektedir. Ancak, bu mikropları birbirinden ayırt edebilmek çoğu zaman meşakkatli bir iş olmaktadır. Mikropların çeşitli özelliklerini anlayan ve taksonomi nüanslarını yorumlayabilen bir uzman bilgisinin gerekmesi ve laboratuvar ihtiyacının olması bu süreci hem maliyetli hem de zaman alıcı yapmaktadır. Bundan dolayı, bilgisayar destekli sistemlerin bu alanda önemi artmış ve günümüzde yapay zeka teknolojileri mikropların sınıflandırılmasında kullanılmaya başlanmıştır. Makine öğrenmesi ve derin öğrenme teknolojilerinin bu alana uygulanmasıyla yüksek seviyede doğruluk skorları elde edilmekte ve biyoçeşitlilikle ilgili değerlendirmeler otomatik bir şekilde yapılabilmektedir. Bu çalışmada da derin öğrenme modellerinden biri olan tekrarlayıcı sinir ağları yapıları kullanılarak, mikropların sınıflandırılması yapılmıştır. Çalışma dört aşamadan meydana gelmiştir. Birinci aşamada, veriler elde edilmiştir. İkinci aşamada bu veriler normalleştirme işlemine tabi tutulmuş ve önişlemden geçirilmiştir. Üçüncü aşamada UKSB ve TSA modelleri tasarlanmış ve sınıflandırılmıştır. Son aşamada ise sınıflandırıcıların performansları doğruluk, kesinlik, duyarlılık, F1-skor ve AUC skoru ile belirlenmiştir. Çalışmanın sonunda TSA sınıflandırıcısı ile %92.53, UKSB sınıflandırıcısıyla ise %99.85 doğruluk skoru elde edilmiştir.
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15
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Carrier TJ, Schmittmann L, Jung S, Pita L, Hentschel U. Maternal provisioning of an obligate symbiont in a sponge. Ecol Evol 2023; 13:e10012. [PMID: 37153023 PMCID: PMC10154371 DOI: 10.1002/ece3.10012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 05/09/2023] Open
Abstract
The transmission of microbes from mother to offspring is an ancient, advantageous, and widespread feature of metazoan life history. Despite this, little is known about the quantitative strategies taken to maintain symbioses across generations. The quantity of maternal microbes that is provided to each offspring through vertical transmission could theoretically be stochastic (no trend), consistent (an optimal range is allocated), or provisioned (a trade-off with fecundity). Examples currently come from animals that release free-living eggs (oviparous) and suggest that offspring are provided a consistent quantity of symbionts. The quantity of maternal microbes that is vertically transmitted in other major reproductive strategies has yet to be assessed. We used the brooding (viviparous) sponge Halichondria panicea to test whether offspring receive quantitatively similar numbers of maternal microbes. We observed that H. panicea has a maternal pool of the obligate symbiont Candidatus Halichondribacter symbioticus and that this maternal pool is provisioned proportionally to reproductive output and allometrically by offspring size. This pattern was not observed for the total bacterial community. Experimental perturbation by antibiotics could not reduce the abundance of Ca. H. symbioticus in larvae, while the total bacterial community could be reduced without affecting the ability of larvae to undergo metamorphosis. A trade-off between offspring size and number is, by definition, maternal provisioning and parallel differences in Ca. H. symbioticus abundance would suggest that this obligate symbiont is also provisioned.
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Affiliation(s)
- Tyler J. Carrier
- GEOMAR Helmholtz Center for Ocean ResearchKielGermany
- Zoological Institute, Christian‐Albrechts University of KielKielGermany
| | | | - Sabrina Jung
- GEOMAR Helmholtz Center for Ocean ResearchKielGermany
| | - Lucía Pita
- GEOMAR Helmholtz Center for Ocean ResearchKielGermany
- Department Marine Biology and OceanographyInstitute of Marine Sciences (ICM‐CSIC)BarcelonaSpain
| | - Ute Hentschel
- GEOMAR Helmholtz Center for Ocean ResearchKielGermany
- Zoological Institute, Christian‐Albrechts University of KielKielGermany
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16
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Seasonal dynamics of a complex cheilostome bryozoan symbiosis: vertical transfer challenged. Sci Rep 2023; 13:375. [PMID: 36611035 PMCID: PMC9825505 DOI: 10.1038/s41598-022-26251-6] [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: 08/10/2022] [Accepted: 12/12/2022] [Indexed: 01/09/2023] Open
Abstract
Symbiotic associations are dynamic systems influenced by both intrinsic and extrinsic factors. Here we describe for the first time the developmental and seasonal changes of the funicular bodies in the bryozoan Dendrobeania fruticosa, which are unique temporary organs of cheilostome bryozoans containing prokaryotic symbionts. Histological and ultrastructural studies showed that these organs undergo strong seasonal modification in the White Sea during the ice-free period. Initially (in June) they play a trophic function and support the development of a large population of bacteria. From June to September, both funicular bodies and bacteria show signs of degradation accompanied by development of presumed virus-like particles (VLPs); these self-organize to hollow spheres inside bacteria and are also detected outside of them. Although the destruction of bacteria coincides with the development of VLPs and spheres, the general picture differs considerably from the known instances of bacteriophagy in bryozoans. We broadly discuss potential routes of bacterial infection in Bryozoa and question the hypothesis of vertical transfer, which, although widely accepted in the literature, is contradicted by molecular, morphological and ecological evidence.
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17
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Zapién-Campos R, Bansept F, Sieber M, Traulsen A. On the effect of inheritance of microbes in commensal microbiomes. BMC Ecol Evol 2022; 22:75. [PMID: 35710335 PMCID: PMC9204957 DOI: 10.1186/s12862-022-02029-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 06/02/2022] [Indexed: 11/10/2022] Open
Abstract
Background Our current view of nature depicts a world where macroorganisms dwell in a landscape full of microbes. Some of these microbes not only transit but establish themselves in or on hosts. Although hosts might be occupied by microbes for most of their lives, a microbe-free stage during their prenatal development seems to be the rule for many hosts. The questions of who the first colonizers of a newborn host are and to what extent these are obtained from the parents follow naturally. Results We have developed a mathematical model to study the effect of the transfer of microbes from parents to offspring. Even without selection, we observe that microbial inheritance is particularly effective in modifying the microbiome of hosts with a short lifespan or limited colonization from the environment, for example by favouring the acquisition of rare microbes. Conclusion By modelling the inheritance of commensal microbes to newborns, our results suggest that, in an eco-evolutionary context, the impact of microbial inheritance is of particular importance for some specific life histories. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02029-2.
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18
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Jorge F, Dheilly NM, Froissard C, Poulin R. Association between parasite microbiomes and caste development and colony structure in a social trematode. Mol Ecol 2022; 31:5608-5617. [PMID: 36004565 PMCID: PMC9826137 DOI: 10.1111/mec.16671] [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: 06/27/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 01/11/2023]
Abstract
Division of labour through the formation of morphologically and functionally distinct castes is a recurring theme in the evolution of animal sociality. The mechanisms driving the differentiation of individuals into distinct castes remain poorly understood, especially for animals forming clonal colonies. We test the association between microbiomes and caste formation within the social trematode Philophthalmus attenuatus, using a metabarcoding approach targeting the bacterial 16S SSU rRNA gene. Clonal colonies of this trematode within snail hosts comprise large reproductive individuals which produce dispersal stages, and small, non-reproducing soldiers which defend the colony against invaders. In colonies extracted directly from field-collected snails, reproductives harboured more diverse bacterial communities than soldiers, and reproductives and soldiers harboured distinct bacterial communities, at all taxonomic levels considered. No single bacterial taxon showed high enough prevalence in either soldiers or reproductives to be singled out as a key driver, indicating that the whole microbial community contributes to these differences. Other colonies were experimentally exposed to antibiotics to alter their bacterial communities, and sampled shortly after treatment and weeks later after allowing for turnover of colony members. At those time points, bacterial communities of the two castes still differed across all antibiotic treatments; however, the caste ratio within colonies changed: after antibiotic disruption and turnover of individuals, new individuals were more likely to become reproductives than in undisturbed control colonies. Our results reveal that each caste has a distinct microbiome; whether the social context affects the microbiota, or whether microbes contribute to modulating the phenotype of individuals, remains to be determined.
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Affiliation(s)
- Fátima Jorge
- Otago Micro and Nano Imaging, Electron Microscopy UnitUniversity of OtagoDunedinNew Zealand
| | - Nolwenn M. Dheilly
- School of Marine and Atmospheric SciencesStony Brook UniversityStony BrookNew YorkUSA,Unité Génétique Virale de Biosécurité, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail ‐ Laboratoire de Ploufragan‐PlouzanéANSESPloufraganFrance
| | | | - Robert Poulin
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
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19
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Henry LP, Ayroles JF. Drosophila melanogaster microbiome is shaped by strict filtering and neutrality along a latitudinal cline. Mol Ecol 2022; 31:5861-5871. [PMID: 36094780 PMCID: PMC9643648 DOI: 10.1111/mec.16692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 01/13/2023]
Abstract
Microbiomes affect many aspects of host biology, but the eco-evolutionary forces that shape their diversity in natural populations remain poorly understood. Geographical gradients, such as latitudinal clines, generate predictable patterns in biodiversity at macroecological scales, but whether these macroscale processes apply to host-microbiome interactions is an open question. To address this question, we sampled the microbiomes of 13 natural populations of Drosophila melanogaster along a latitudinal cline in the eastern United States. The microbiomes were surprisingly consistent across the cline, as latitude did not predict either alpha or beta diversity. Only a narrow taxonomic range of bacteria were present in all microbiomes, indicating that strict taxonomic filtering by the host and neutral ecological dynamics are the primary factors shaping the fly microbiome. Our findings reveal the complexity of eco-evolutionary interactions shaping microbial variation in D. melanogaster and highlight the need for additional sampling of the microbiomes in natural populations along environmental gradients.
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Affiliation(s)
- Lucas P Henry
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Julien F Ayroles
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
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20
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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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21
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Sato Y, Wippler J, Wentrup C, Ansorge R, Sadowski M, Gruber-Vodicka H, Dubilier N, Kleiner M. Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium. MICROBIOME 2022; 10:178. [PMID: 36273146 PMCID: PMC9587655 DOI: 10.1186/s40168-022-01372-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/15/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Many animals live in intimate associations with a species-rich microbiome. A key factor in maintaining these beneficial associations is fidelity, defined as the stability of associations between hosts and their microbiota over multiple host generations. Fidelity has been well studied in terrestrial hosts, particularly insects, over longer macroevolutionary time. In contrast, little is known about fidelity in marine animals with species-rich microbiomes at short microevolutionary time scales, that is at the level of a single host population. Given that natural selection acts most directly on local populations, studies of microevolutionary partner fidelity are important for revealing the ecological and evolutionary processes that drive intimate beneficial associations within animal species. RESULTS In this study on the obligate symbiosis between the gutless marine annelid Olavius algarvensis and its consortium of seven co-occurring bacterial symbionts, we show that partner fidelity varies across symbiont species from strict to absent over short microevolutionary time. Using a low-coverage sequencing approach that has not yet been applied to microbial community analyses, we analysed the metagenomes of 80 O. algarvensis individuals from the Mediterranean and compared host mitochondrial and symbiont phylogenies based on single-nucleotide polymorphisms across genomes. Fidelity was highest for the two chemoautotrophic, sulphur-oxidizing symbionts that dominated the microbial consortium of all O. algarvensis individuals. In contrast, fidelity was only intermediate to absent in the sulphate-reducing and spirochaetal symbionts with lower abundance. These differences in fidelity are likely driven by both selective and stochastic forces acting on the consistency with which symbionts are vertically transmitted. CONCLUSIONS We hypothesize that variable degrees of fidelity are advantageous for O. algarvensis by allowing the faithful transmission of their nutritionally most important symbionts and flexibility in the acquisition of other symbionts that promote ecological plasticity in the acquisition of environmental resources. Video Abstract.
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Affiliation(s)
- Yui Sato
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany.
| | - Juliane Wippler
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| | - Cecilia Wentrup
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| | - Rebecca Ansorge
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, NR4 7UQ, UK
| | - Miriam Sadowski
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| | - Harald Gruber-Vodicka
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359, Bremen, Germany.
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
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22
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Engelberts JP, Abdul Wahab MA, Maldonado M, Rix L, Marangon E, Robbins SJ, Wagner M, Webster NS. Microbes from Mum: symbiont transmission in the tropical reef sponge Ianthella basta. ISME COMMUNICATIONS 2022; 2:90. [PMID: 37938734 PMCID: PMC9723589 DOI: 10.1038/s43705-022-00173-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 05/28/2023]
Abstract
Most marine sponge species harbour distinct communities of microorganisms which contribute to various aspects of their host's health and physiology. In addition to their key roles in nutrient transformations and chemical defence, these symbiotic microbes can shape sponge phenotype by mediating important developmental stages and influencing the environmental tolerance of the host. However, the characterisation of each microbial taxon throughout a sponge's life cycle remains challenging, with several sponge species hosting up to 3000 distinct microbial species. Ianthella basta, an abundant broadcast spawning species in the Indo-Pacific, is an emerging model for sponge symbiosis research as it harbours only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium. Here, we successfully spawned Ianthella basta, characterised its mode of reproduction, and used 16S rRNA gene amplicon sequencing, fluorescence in situ hybridisation, and transmission electron microscopy to characterise the microbial community throughout its life cycle. We confirmed I. basta as being gonochoric and showed that the three dominant symbionts, which together make up >90% of the microbiome according to 16S rRNA gene abundance, are vertically transmitted from mother to offspring by a unique method involving encapsulation in the peri-oocytic space, suggesting an obligate relationship between these microbes and their host.
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Affiliation(s)
- J Pamela Engelberts
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
| | | | - Manuel Maldonado
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | - Laura Rix
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Emma Marangon
- Australian Institute of Marine Science, Townsville, QLD, Australia
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Steven J Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Nicole S Webster
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- Australian Antarctic Division, Kingston, TAS, Australia
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23
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Kim H, Jeon J, Lee KK, Lee YH. Longitudinal transmission of bacterial and fungal communities from seed to seed in rice. Commun Biol 2022; 5:772. [PMID: 35915150 PMCID: PMC9343636 DOI: 10.1038/s42003-022-03726-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/14/2022] [Indexed: 12/22/2022] Open
Abstract
Vertical transmission of microbes is crucial for the persistence of host-associated microbial communities. Although vertical transmission of seed microbes has been reported from diverse plants, ecological mechanisms and dynamics of microbial communities from parent to progeny remain scarce. Here we reveal the veiled ecological mechanism governing transmission of bacterial and fungal communities in rice across two consecutive seasons. We identify 29 bacterial and 34 fungal members transmitted across generations. Abundance-based regression models allow to classify colonization types of the microbes. We find that they are late colonizers dominating each community at the ripening stage. Ecological models further show that the observed temporal colonization patterns are affected by niche change and neutrality. Source-sink modeling reveals that parental seeds and stem endosphere are major origins of progeny seed microbial communities. This study gives empirical evidence for ecological mechanism and dynamics of bacterial and fungal communities as an ecological continuum during seed-to-seed transmission.
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Affiliation(s)
- Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Republic of Korea.,Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Kiseok Kieth Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.,Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL, 60637, USA
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea. .,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Republic of Korea. .,Center for Plant Microbiome Research, Seoul National University, Seoul, 08826, Republic of Korea. .,Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea. .,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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24
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Vad J, Duran Suja L, Summers S, Henry TB, Roberts JM. Marine Sponges in a Snowstorm – Extreme Sensitivity of a Sponge Holobiont to Marine Oil Snow and Chemically Dispersed Oil Pollution. Front Microbiol 2022; 13:909853. [PMID: 35910618 PMCID: PMC9335075 DOI: 10.3389/fmicb.2022.909853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Holobionts formed by a host organism and associated symbionts are key biological units in marine ecosystems where they are responsible for fundamental ecosystem services. Therefore, understanding anthropogenic impacts on holobionts is essential. Sponges (Phylum Porifera) are ideal holobiont models. They host a complex microbial community and provide ecosystem services including nutrient cycling. At bathyal depths, sponges can accumulate forming dense sponge ground habitats supporting biodiverse associated communities. However, the impacts of spilled oil and dispersants on sponge grounds cannot be understood without considering exposures mediated through sponge filtration of marine snow particles. To examine this, we exposed the model sponge Halichondria panicea to oil, dispersant and “marine oil snow” contaminated seawater and elucidate the complex molecular response of the holobiont through metatranscriptomics. While the host response included detoxification and immune response pathways, the bacterial symbiotic response differed and was at least partially the result of a change in the host environment rather than a direct response to hydrocarbon exposure. As the sponge host reduced its pumping activity and internal tissue oxygen levels declined, the symbionts changed their metabolism from aerobic to anaerobic pathways possibly via quorum sensing. Furthermore, we found evidence of hydrocarbon degradation by sponge symbionts, but sponge mortality (even when exposed to low concentrations of hydrocarbons) implied this may not provide the holobiont with sufficient resilience against contaminants. Given the continued proposed expansion of hydrocarbon production into deep continental shelf and slope settings where sponge grounds form significant habitats it is important that dispersant use is minimised and that environmental impact assessments carefully consider the vulnerability of sponge holobionts.
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Affiliation(s)
- Johanne Vad
- Changing Oceans Group, School of Geosciences, The University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Johanne Vad,
| | - Laura Duran Suja
- Changing Oceans Group, School of Geosciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen Summers
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Theodore B. Henry
- School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Riccarton, United Kingdom
| | - J. Murray Roberts
- Changing Oceans Group, School of Geosciences, The University of Edinburgh, Edinburgh, United Kingdom
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25
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Wang P, Li M, Dong L, Zhang C, Xie W. Comparative Genomics of Thaumarchaeota From Deep-Sea Sponges Reveal Their Niche Adaptation. Front Microbiol 2022; 13:869834. [PMID: 35859738 PMCID: PMC9289680 DOI: 10.3389/fmicb.2022.869834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
Thaumarchaeota account for a large portion of microbial symbionts in deep-sea sponges and are even dominant in some cases. In this study, we investigated three new sponge-associated Thaumarchaeota from the deep West Pacific Ocean. Thaumarchaeota were found to be the most dominant phylum in this sponge by both prokaryotic 16S rRNA amplicons and metagenomic sequencing. Fifty-seven published Thaumarchaeota genomes from sponges and other habitats were included for genomic comparison. Similar to shallow sponge-associated Thaumarchaeota, those Thaumarchaeota in deep-sea sponges have extended genome sizes and lower coding density compared with their free-living lineages. Thaumarchaeota in deep-sea sponges were specifically enriched in genes related to stress adapting, symbiotic adhesion and stability, host–microbe interaction and protein transportation. The genes involved in defense mechanisms, such as the restriction-modification system, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system, and toxin-antitoxin system were commonly enriched in both shallow and deep sponge-associated Thaumarchaeota. Our study demonstrates the significant effects of both depth and symbiosis on forming genomic characteristics of Thaumarchaeota, and provides novel insights into their niche adaptation in deep-sea sponges.
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Affiliation(s)
- Peng Wang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Minchun Li
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Liang Dong
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Cheng Zhang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Wei Xie
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- *Correspondence: Wei Xie,
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26
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Björk JR, Dasari MR, Roche K, Grieneisen L, Gould TJ, Grenier JC, Yotova V, Gottel N, Jansen D, Gesquiere LR, Gordon JB, Learn NH, Wango TL, Mututua RS, Kinyua Warutere J, Siodi L, Mukherjee S, Barreiro LB, Alberts SC, Gilbert JA, Tung J, Blekhman R, Archie EA. Synchrony and idiosyncrasy in the gut microbiome of wild baboons. Nat Ecol Evol 2022; 6:955-964. [PMID: 35654895 PMCID: PMC9271586 DOI: 10.1038/s41559-022-01773-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/20/2022] [Indexed: 01/04/2023]
Abstract
Human gut microbial dynamics are highly individualized, making it challenging to link microbiota to health and to design universal microbiome therapies. This individuality is typically attributed to variation in host genetics, diets, environments and medications but it could also emerge from fundamental ecological forces that shape microbiota more generally. Here, we leverage extensive gut microbial time series from wild baboons-hosts who experience little interindividual dietary and environmental heterogeneity-to test whether gut microbial dynamics are synchronized across hosts or largely idiosyncratic. Despite their shared lifestyles, baboon microbiota were only weakly synchronized. The strongest synchrony occurred among baboons living in the same social group, probably because group members range over the same habitat and simultaneously encounter the same sources of food and water. However, this synchrony was modest compared to each host's personalized dynamics. In support, host-specific factors, especially host identity, explained, on average, more than three times the deviance in longitudinal dynamics compared to factors shared with social group members and ten times the deviance of factors shared across the host population. These results contribute to mounting evidence that highly idiosyncratic gut microbiomes are not an artefact of modern human environments and that synchronizing forces in the gut microbiome (for example, shared environments, diets and microbial dispersal) are not strong enough to overwhelm key drivers of microbiome personalization, such as host genetics, priority effects, horizontal gene transfer and functional redundancy.
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Affiliation(s)
- Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
| | - Mauna R Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Kim Roche
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
| | - Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Trevor J Gould
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Jean-Christophe Grenier
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec, Canada
- Research Center, Montreal Heart Institute, Montréal, Quebec, Canada
| | - Vania Yotova
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec, Canada
| | - Neil Gottel
- Department of Pediatrics and the Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, USA
| | - David Jansen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | | | | | - Niki H Learn
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Tim L Wango
- Amboseli Baboon Research Project, Amboseli National Park, Amboseli, Kenya
- The Department of Veterinary Anatomy and Animal Physiology, University of Nairobi, Nairobi, Kenya
| | - Raphael S Mututua
- Amboseli Baboon Research Project, Amboseli National Park, Amboseli, Kenya
| | - J Kinyua Warutere
- Amboseli Baboon Research Project, Amboseli National Park, Amboseli, Kenya
| | - Long'ida Siodi
- Amboseli Baboon Research Project, Amboseli National Park, Amboseli, Kenya
| | - Sayan Mukherjee
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA
| | - Luis B Barreiro
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Duke University Population Research Institute, Duke University, Durham, NC, USA
| | - Jack A Gilbert
- Department of Pediatrics and the Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Duke University Population Research Institute, Duke University, Durham, NC, USA
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
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27
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Amelia TSM, Suaberon FAC, Vad J, Fahmi ADM, Saludes JP, Bhubalan K. Recent Advances of Marine Sponge-Associated Microorganisms as a Source of Commercially Viable Natural Products. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:492-512. [PMID: 35567600 DOI: 10.1007/s10126-022-10130-2] [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: 12/02/2021] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Many industrially significant compounds have been derived from natural products in the environment. Research efforts so far have contributed to the discovery of beneficial natural products that have improved the quality of life on Earth. As one of the sources of natural products, marine sponges have been progressively recognised as microbial hotspots with reports of the sponges harbouring diverse microbial assemblages, genetic material, and metabolites with multiple industrial applications. Therefore, this paper aims at reviewing the recent literature (primarily published between 2016 and 2022) on the types and functions of natural products synthesised by sponge-associated microorganisms, thereby helping to bridge the gap between research and industrial applications. The metabolites that have been derived from sponge-associated microorganisms, mostly bacteria, fungi, and algae, have shown application prospects especially in medicine, cosmeceutical, environmental protection, and manufacturing industries. Sponge bacteria-derived natural products with medical properties harboured anticancer, antibacterial, antifungal, and antiviral functions. Efforts in re-identifying the origin of known and future sponge-sourced natural products would further clarify the roles and significance of microbes within marine sponges.
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Affiliation(s)
- Tan Suet May Amelia
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Ferr Angelus C Suaberon
- Center for Natural Drug Discovery & Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines
| | - Johanne Vad
- Changing Oceans Research Group, School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Afiq Durrani Mohd Fahmi
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
- Eco-Innovation Research Interest Group, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Jonel P Saludes
- Center for Natural Drug Discovery & Development (CND3), University of San Agustin, 5000, Iloilo City, Philippines
- Department of Chemistry, University of San Agustin, 5000, Iloilo City, Philippines
- Department of Science and Technology, Balik Scientist Program, Philippine Council for Health Research & Development (PCHRD), Bicutan, 1631, Taguig, Philippines
| | - Kesaven Bhubalan
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
- Eco-Innovation Research Interest Group, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
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28
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Unzueta-Martínez A, Scanes E, Parker LM, Ross PM, O'Connor W, Bowen JL. Microbiomes of the Sydney Rock Oyster are acquired through both vertical and horizontal transmission. Anim Microbiome 2022; 4:32. [PMID: 35590396 PMCID: PMC9118846 DOI: 10.1186/s42523-022-00186-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/07/2022] [Indexed: 11/10/2022] Open
Abstract
Background The term holobiont is widely accepted to describe animal hosts and their associated microorganisms. The genomes of all that the holobiont encompasses, are termed the hologenome and it has been proposed as a unit of selection in evolution. To demonstrate that natural selection acts on the hologenome, a significant portion of the associated microbial genomes should be transferred between generations. Using the Sydney Rock Oyster (Saccostrea glomerata) as a model, we tested if the microbes of this broadcast spawning species could be passed down to the next generation by conducting single parent crosses and tracking the microbiome from parent to offspring and throughout early larval stages using 16S rRNA gene amplicon sequencing. From each cross, we sampled adult tissues (mantle, gill, stomach, gonad, eggs or sperm), larvae (D-veliger, umbo, eyed pediveliger, and spat), and the surrounding environment (water and algae feed) for microbial community analysis. Results We found that each larval stage has a distinct microbiome that is partially influenced by their parental microbiome, particularly the maternal egg microbiome. We also demonstrate the presence of core microbes that are consistent across all families, persist throughout early life stages (from eggs to spat), and are not detected in the microbiomes of the surrounding environment. In addition to the core microbiomes that span all life cycle stages, there is also evidence of environmentally acquired microbial communities, with earlier larval stages (D-veliger and umbo), more influenced by seawater microbiomes, and later larval stages (eyed pediveliger and spat) dominated by microbial members that are specific to oysters and not detected in the surrounding environment. Conclusion Our study characterized the succession of oyster larvae microbiomes from gametes to spat and tracked selected members that persisted across multiple life stages. Overall our findings suggest that both horizontal and vertical transmission routes are possible for the complex microbial communities associated with a broadcast spawning marine invertebrate. We demonstrate that not all members of oyster-associated microbiomes are governed by the same ecological dynamics, which is critical for determining what constitutes a hologenome. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00186-9.
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Affiliation(s)
- Andrea Unzueta-Martínez
- Department of Marine and Environmental Science, Northeastern University, Nahant, MA, 01908, USA. .,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Elliot Scanes
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia.,Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Laura M Parker
- School of Biological, Earth and Environmental Sciences, The University of New South Wales, Kensington, NSW, 2052, Australia
| | - Pauline M Ross
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Wayne O'Connor
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, Taylors Beach, NSW, 2316, Australia
| | - Jennifer L Bowen
- Department of Marine and Environmental Science, Northeastern University, Nahant, MA, 01908, USA
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29
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Carrier TJ, Maldonado M, Schmittmann L, Pita L, Bosch TCG, Hentschel U. Symbiont transmission in marine sponges: reproduction, development, and metamorphosis. BMC Biol 2022; 20:100. [PMID: 35524305 PMCID: PMC9077847 DOI: 10.1186/s12915-022-01291-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 04/07/2022] [Indexed: 11/10/2022] Open
Abstract
Marine sponges (phylum Porifera) form symbioses with diverse microbial communities that can be transmitted between generations through their developmental stages. Here, we integrate embryology and microbiology to review how symbiotic microorganisms are transmitted in this early-diverging lineage. We describe that vertical transmission is widespread but not universal, that microbes are vertically transmitted during a select developmental window, and that properties of the developmental microbiome depends on whether a species is a high or low microbial abundance sponge. Reproduction, development, and symbiosis are thus deeply rooted, but why these partnerships form remains the central and elusive tenet of these developmental symbioses.
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Affiliation(s)
- Tyler J Carrier
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
- Zoological Institute, University of Kiel, Kiel, Germany.
| | - Manuel Maldonado
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | | | - Lucía Pita
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | | | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Zoological Institute, University of Kiel, Kiel, Germany
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30
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Oceanographic setting influences the prokaryotic community and metabolome in deep-sea sponges. Sci Rep 2022; 12:3356. [PMID: 35233042 PMCID: PMC8888554 DOI: 10.1038/s41598-022-07292-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/16/2022] [Indexed: 11/09/2022] Open
Abstract
Marine sponges (phylum Porifera) are leading organisms for the discovery of bioactive compounds from nature. Their often rich and species-specific microbiota is hypothesised to be producing many of these compounds. Yet, environmental influences on the sponge-associated microbiota and bioactive compound production remain elusive. Here, we investigated the changes of microbiota and metabolomes in sponges along a depth range of 1232 m. Using 16S rRNA gene amplicon sequencing and untargeted metabolomics, we assessed prokaryotic and chemical diversities in three deep-sea sponge species: Geodia barretti, Stryphnus fortis, and Weberella bursa. Both prokaryotic communities and metabolome varied significantly with depth, which we hypothesized to be the effect of different water masses. Up to 35.5% of microbial ASVs (amplicon sequence variants) showed significant changes with depth while phylum-level composition of host microbiome remained unchanged. The metabolome varied with depth, with relative quantities of known bioactive compounds increasing or decreasing strongly. Other metabolites varying with depth were compatible solutes regulating osmolarity of the cells. Correlations between prokaryotic community and the bioactive compounds in G. barretti suggested members of Acidobacteria, Proteobacteria, Chloroflexi, or an unclassified prokaryote as potential producers.
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31
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Petrullo L, Baniel A, Jorgensen MJ, Sams S, Snyder-Mackler N, Lu A. The early life microbiota mediates maternal effects on offspring growth in a nonhuman primate. iScience 2022; 25:103948. [PMID: 35265817 PMCID: PMC8898918 DOI: 10.1016/j.isci.2022.103948] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/06/2022] [Accepted: 02/15/2022] [Indexed: 01/13/2023] Open
Abstract
Maternal parity can impact offspring growth, but the mechanisms driving this effect are unclear. Here, we test the hypothesis that vertically transmitted microbiota may be one potential mechanism. We analyzed 118 fecal and milk samples from mother-offspring vervet monkey dyads across the first 6 months of life. Despite poorer milk production, offspring born to low parity females grew larger than their counterparts. These offspring exhibited reduced alpha diversity in the first days of life, stronger seeding of maternal milk microbiota, Bacteroides fragilis dominance, and a greater abundance of glycan utilization pathways. Moreover, the attainment of greater body mass by 6 months of age was mediated by reduced early life alpha diversity and B. fragilis dominance. This work demonstrates that the establishment of a specialized, milk-oriented gut microbiota promotes infant growth and suggests an evolutionarily conserved developmental role of B. fragilis in primates.
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Affiliation(s)
- Lauren Petrullo
- Department of Psychology, University of Michigan, Ann Arbor, MI 48109, USA,Corresponding author
| | - Alice Baniel
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA,School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Matthew J. Jorgensen
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Sierra Sams
- Paragon Genomics, Hayward, CA 94545, USA,Department of Psychology, University of Washington, Seattle, WA 98195, USA
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85281, USA,School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA,Department of Psychology, University of Washington, Seattle, WA 98195, USA,Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Amy Lu
- Department of Anthropology, Stony Brook University, Stony Brook, NY 11794, USA
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32
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Cristi A, Parada-Pozo G, Morales-Vicencio F, Cárdenas CA, Trefault N. Variability in Host Specificity and Functional Potential of Antarctic Sponge-Associated Bacterial Communities. Front Microbiol 2022; 12:771589. [PMID: 35095792 PMCID: PMC8792898 DOI: 10.3389/fmicb.2021.771589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/02/2021] [Indexed: 12/30/2022] Open
Abstract
Sponge-associated microorganisms are essential for sponge survival. They play an important role in recycling nutrients and, therefore, in the maintenance of the ecosystem. These microorganisms are diverse, species-specific, and different from those in the surrounding seawater. Bacterial sponge symbionts have been extensively studied in the tropics; however, little is known about these microorganisms in sponges from high-latitude environments. Sponges can cover up to 80% of the benthos in Antarctica and are crucial architects for the marine food web. In this study, we present analyses of the bacterial symbionts of three sponges: Haliclona (Rhizoniera) sp., Hymeniacidon torquata, and Isodictya kerguelenensis from the Western Antarctic Peninsula (WAP) with the aim to determine variations on the specificity of the bacteria–sponge interactions and potential signatures on their predicted functional profiles. We use high-throughput 16S rRNA gene sequencing of 30 sponge individuals inhabiting South Bay (Palmer Archipelago, WAP) to describe their microbiome taxonomy and diversity and predict potential functional profiles based on this marker gene. Our work shows similar bacterial community composition profiles among the same sponge species, although the symbiotic relationship is not equally conserved among the three Antarctic sponges. The number of species-specific core operational taxonomic units (OTUs) of these Antarctic sponges was low, with important differences between the total abundance accounted for these OTUs. Only eight OTUs were shared between the three sponge species. Analyses of the functional potential revealed that despite the high host–symbiont specificity, the inferred functions are conserved among these microbiomes, although with differences in the abundance of specific functions. H. torquata showed the highest level of intra-specificity and a higher potential of pathways related to energy metabolism, metabolisms of terpenoids and polyketides, and biosynthesis of other secondary metabolites. Overall, this work shows variations in the specificity of the sponge-associated bacterial communities, differences in how hosts and symbionts establish their relations, and in their potential functional capabilities.
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Affiliation(s)
- Antonia Cristi
- Centro GEMA – Genómica, Ecología y Medio Ambiente, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- Department of Marine Science, University of Otago, Dunedin, New Zealand
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Génesis Parada-Pozo
- Centro GEMA – Genómica, Ecología y Medio Ambiente, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Felipe Morales-Vicencio
- Centro GEMA – Genómica, Ecología y Medio Ambiente, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - César A. Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | - Nicole Trefault
- Centro GEMA – Genómica, Ecología y Medio Ambiente, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- *Correspondence: Nicole Trefault,
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Natural selection for imprecise vertical transmission in host-microbiota systems. Nat Ecol Evol 2022; 6:77-87. [PMID: 34949814 PMCID: PMC9901532 DOI: 10.1038/s41559-021-01593-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/19/2021] [Indexed: 02/08/2023]
Abstract
How and when the microbiome modulates host adaptation remains an evolutionary puzzle, despite evidence that the extended genetic repertoire of the microbiome can shape host phenotypes and fitness. One complicating factor is that the microbiome is often transmitted imperfectly across host generations, leading to questions about the degree to which the microbiome contributes to host adaptation. Here, using an evolutionary model, we demonstrate that decreasing vertical transmission fidelity can increase microbiome variation, and thus phenotypic variation, across hosts. When the most beneficial microbial genotypes change unpredictably from one generation to the next (for example, in variable environments), hosts can maximize fitness by increasing the microbiome variation among offspring, as this improves the chance of there being an offspring with the right microbial combination for the next generation. Imperfect vertical transmission can therefore be adaptive in varying environments. We characterize how selection on vertical transmission is shaped by environmental conditions, microbiome changes during host development and the contribution of other factors to trait variation. We illustrate how environmentally dependent microbial effects can favour intermediate transmission and set our results in the context of examples from natural systems. We also suggest research avenues to empirically test our predictions. Our model provides a basis to understand the evolutionary pathways that potentially led to the wide diversity of microbe transmission patterns found in nature.
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Rosenberg E, Zilber-Rosenberg I. Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations. Microorganisms 2021; 10:microorganisms10010070. [PMID: 35056519 PMCID: PMC8780831 DOI: 10.3390/microorganisms10010070] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Microbiomes are transmitted between generations by a variety of different vertical and/or horizontal modes, including vegetative reproduction (vertical), via female germ cells (vertical), coprophagy and regurgitation (vertical and horizontal), physical contact starting at birth (vertical and horizontal), breast-feeding (vertical), and via the environment (horizontal). Analyses of vertical transmission can result in false negatives (failure to detect rare microbes) and false positives (strain variants). In humans, offspring receive most of their initial gut microbiota vertically from mothers during birth, via breast-feeding and close contact. Horizontal transmission is common in marine organisms and involves selectivity in determining which environmental microbes can colonize the organism's microbiome. The following arguments are put forth concerning accurate microbial transmission: First, the transmission may be of functions, not necessarily of species; second, horizontal transmission may be as accurate as vertical transmission; third, detection techniques may fail to detect rare microbes; lastly, microbiomes develop and reach maturity with their hosts. In spite of the great variation in means of transmission discussed in this paper, microbiomes and their functions are transferred from one generation of holobionts to the next with fidelity. This provides a strong basis for each holobiont to be considered a unique biological entity and a level of selection in evolution, largely maintaining the uniqueness of the entity and conserving the species from one generation to the next.
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Baldassarre L, Levy S, Bar-Shalom R, Steindler L, Lotan T, Fraune S. Contribution of Maternal and Paternal Transmission to Bacterial Colonization in Nematostella vectensis. Front Microbiol 2021; 12:726795. [PMID: 34707584 PMCID: PMC8544946 DOI: 10.3389/fmicb.2021.726795] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/08/2021] [Indexed: 12/15/2022] Open
Abstract
Microbial communities confer multiple beneficial effects to their multicellular hosts. To evaluate the evolutionary and ecological implications of the animal-microbe interactions, it is essential to understand how bacterial colonization is secured and maintained during the transition from one generation to the next. However, the mechanisms of symbiont transmission are poorly studied for many species, especially in marine environments, where the surrounding water constitutes an additional source of microbes. Nematostella vectensis, an estuarine cnidarian, has recently emerged as model organism for studies on host-microbes interactions. Here, we use this model organism to study the transmission of bacterial colonizers, evaluating the contribution of parental and environmental transmission to the establishment of bacterial communities of the offspring. We induced spawning in adult male and female polyps of N. vectensis and used their gametes for five individual fertilization experiments. While embryos developed into primary polyps, we sampled each developmental stage and its corresponding medium samples. By analyzing the microbial community compositions of all samples through 16S rRNA gene amplicon sequencing, we showed that all host tissues harbor microbiota significantly different from the surrounding medium. Interestingly, oocytes and sperms are associated with distinct bacterial communities, indicating the specific vertical transmission of bacterial colonizers by the gametes. These differences were consistent among all the five families analyzed. By overlapping the identified bacterial ASVs associated with gametes, offspring and parents, we identified specific bacterial ASVs that are well supported candidates for vertical transmission via mothers and fathers. This is the first study investigating bacteria transmission in N. vectensis, and among few on marine spawners that do not brood larvae. Our results shed light on the consistent yet distinct maternal and paternal transfer of bacterial symbionts along the different life stages and generations of an aquatic invertebrate.
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Affiliation(s)
- Laura Baldassarre
- Institute for Zoology and Organismic Interactions, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany.,Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Sezione di Oceanografia, Trieste, Italy
| | - Shani Levy
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Rinat Bar-Shalom
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Tamar Lotan
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Sebastian Fraune
- Institute for Zoology and Organismic Interactions, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
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Vad J, Barnhill KA, Kazanidis G, Roberts JM. Human impacts on deep-sea sponge grounds: Applying environmental omics to monitoring. ADVANCES IN MARINE BIOLOGY 2021; 89:53-78. [PMID: 34583815 DOI: 10.1016/bs.amb.2021.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Sponges (Phylum Porifera) are the oldest extant Metazoans. In the deep sea, sponges can occur at high densities forming habitats known as sponge grounds. Sponge grounds can extend over large areas of up to hundreds of km2 and are biodiversity hotspots. However, as human activities, including deep-water hydrocarbon extraction, continue to expand into areas harbouring sponge grounds, understanding how anthropogenic impacts affect sponges and the ecosystem services they provide at multiple biological scales (community, individual and (sub)cellular levels) is key for achieving sustainable management. This chapter (1) provides an update to the chapter of Advances in Marine Biology Volume 79 entitled "Potential Impacts of Offshore Oil and Gas Activities on Deep-Sea Sponges and the Habitats They Form" and (2) discusses the use of omics as a future tool for deep-sea ecosystem monitoring. While metagenomics and (meta)transcriptomics studies have contributed to improve our understanding of sponge biology in recent years, metabolomics analysis has mostly been used to identify natural products. The sponge metabolome, therefore, remains vastly unknown despite the fact that the metabolome is a key link between the genotype and phenotype, giving us a unique new insight to how key components of an ecosystem are functioning. As the fraction of the metabolome released into the seawater, the sponge exometabolome has only just started to be characterised in comparative environmental metabolomic studies. Yet, the sponge exometabolome constitute a unique opportunity for the identification of biomarkers of sponge health as compounds can be measured in seawater, bypassing the need for physical samples which can still be difficult to collect in the deep sea. Within sponge grounds, the characterisation of a shared sponge exometabolome could lead to the identification of biomarkers of ecosystem functioning and overall health. Challenges remain in establishing omics approaches in environmental monitoring but constant technological advances and reduction in costs means these techniques will become widely available in the future.
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Affiliation(s)
- Johanne Vad
- Changing Ocean Research Group, School of Geosciences, University of Edinburgh, Edinburgh, United Kingdom.
| | - Kelsey Archer Barnhill
- Changing Ocean Research Group, School of Geosciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Georgios Kazanidis
- Changing Ocean Research Group, School of Geosciences, University of Edinburgh, Edinburgh, United Kingdom
| | - J Murray Roberts
- Changing Ocean Research Group, School of Geosciences, University of Edinburgh, Edinburgh, United Kingdom
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Leech T, McDowall L, Hopkins KP, Sait SM, Harrison XA, Bretman A. Social environment drives sex and age-specific variation in Drosophila melanogaster microbiome composition and predicted function. Mol Ecol 2021; 30:5831-5843. [PMID: 34494339 DOI: 10.1111/mec.16149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 08/05/2021] [Accepted: 08/20/2021] [Indexed: 12/25/2022]
Abstract
Social environments influence multiple traits of individuals including immunity, stress and ageing, often in sex-specific ways. The composition of the microbiome (the assemblage of symbiotic microorganisms within a host) is determined by environmental factors and the host's immune, endocrine and neural systems. The social environment could alter host microbiomes extrinsically by affecting transmission between individuals, probably promoting homogeneity in the microbiome of social partners. Alternatively, intrinsic effects arising from interactions between the microbiome and host physiology (the microbiota-gut-brain axis) could translate social stress into dysbiotic microbiomes, with consequences for host health. We investigated how manipulating social environments during larval and adult life-stages altered the microbiome composition of Drosophila melanogaster fruit flies. We used social contexts that particularly alter the development and lifespan of males, predicting that any intrinsic social effects on the microbiome would therefore be sex-specific. The presence of adult males during the larval stage significantly altered the microbiome of pupae of both sexes. In adults, same-sex grouping increased bacterial diversity in both sexes. Importantly, the microbiome community structure of males was more sensitive to social contact at older ages, an effect partially mitigated by housing focal males with young rather than coaged groups. Functional analyses suggest that these microbiome changes impact ageing and immune responses. This is consistent with the hypothesis that the substantial effects of the social environment on individual health are mediated through intrinsic effects on the microbiome, and provides a model for understanding the mechanistic basis of the microbiota-gut-brain axis.
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Affiliation(s)
- Thomas Leech
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Max Planck Institute for Biology of Ageing, Köln, Germany
| | - Laurin McDowall
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,School of Life Sciences, University of Dundee, Dundee, UK
| | - Kevin P Hopkins
- Institute of Zoology, Zoological Society of London, London, UK
| | - Steven M Sait
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Xavier A Harrison
- Institute of Zoology, Zoological Society of London, London, UK.,Centre for Ecology & Conservation, University of Exeter, Penryn, UK
| | - Amanda Bretman
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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Carrier TJ, Beaulieu SE, Mills SW, Mullineaux LS, Reitzel AM. Larvae of Deep-Sea Invertebrates Harbor Low-Diversity Bacterial Communities. THE BIOLOGICAL BULLETIN 2021; 241:65-76. [PMID: 34436969 DOI: 10.1086/715669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
AbstractMicrobial symbionts are a common life-history character of marine invertebrates and their developmental stages. Communities of bacteria that associate with the eggs, embryos, and larvae of coastal marine invertebrates tend to be species specific and correlate with aspects of host biology and ecology. The richness of bacteria associated with the developmental stages of coastal marine invertebrates spans four orders of magnitude, from single mutualists to thousands of unique taxa. This understanding stems predominately from the developmental stages of coastal species. If they are broadly representative of marine invertebrates, then we may expect deep-sea species to associate with bacterial communities that are similar in diversity. To test this, we used amplicon sequencing to profile the bacterial communities of invertebrate larvae from multiple taxonomic groups (annelids, molluscs, crustaceans) collected from 2500 to 3670 m in depth in near-bottom waters near hydrothermal vents in 3 different regions of the Pacific Ocean (the East Pacific Rise, the Mariana Back-Arc, and the Pescadero Basin). We find that larvae of deep-sea invertebrates associate with low-diversity bacterial communities (~30 bacterial taxa) that lack specificity between taxonomic groups. The diversity of these communities is estimated to be ~7.9 times lower than that of coastal invertebrate larvae, but this result depends on the taxonomic group. Associating with a low-diversity community may imply that deep-sea invertebrate larvae do not have a strong reliance on a microbiome and that the hypothesized lack of symbiotic contributions would differ from expectations for larvae of coastal marine invertebrates.
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39
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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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40
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Dittami SM, Arboleda E, Auguet JC, Bigalke A, Briand E, Cárdenas P, Cardini U, Decelle J, Engelen AH, Eveillard D, Gachon CMM, Griffiths SM, Harder T, Kayal E, Kazamia E, Lallier FH, Medina M, Marzinelli EM, Morganti TM, Núñez Pons L, Prado S, Pintado J, Saha M, Selosse MA, Skillings D, Stock W, Sunagawa S, Toulza E, Vorobev A, Leblanc C, Not F. A community perspective on the concept of marine holobionts: current status, challenges, and future directions. PeerJ 2021; 9:e10911. [PMID: 33665032 PMCID: PMC7916533 DOI: 10.7717/peerj.10911] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/16/2021] [Indexed: 12/19/2022] Open
Abstract
Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.
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Affiliation(s)
- Simon M Dittami
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Enrique Arboleda
- FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - Arite Bigalke
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Enora Briand
- Laboratoire Phycotoxines, Ifremer, Nantes, France
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Ulisse Cardini
- Integrative Marine Ecology Dept, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Johan Decelle
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRA, Grenoble, France
| | | | - Damien Eveillard
- Laboratoire des Sciences Numériques de Nantes (LS2N), Université de Nantes, CNRS, Nantes, France
| | - Claire M M Gachon
- Scottish Marine Institute, Scottish Association for Marine Science, Oban, United Kingdom
| | - Sarah M Griffiths
- School of Science and the Environment, Manchester Metropolitan University, Manchester, United Kingdom
| | | | - Ehsan Kayal
- FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - François H Lallier
- Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, United States of America
| | - Ezequiel M Marzinelli
- Ecology and Environment Research Centre, The University of Sydney, Sydney, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Sydney Institute of Marine Science, Mosman, Australia
| | | | - Laura Núñez Pons
- Section Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Soizic Prado
- Molecules of Communication and Adaptation of Microorganisms (UMR 7245), National Museum of Natural History, CNRS, Paris, France
| | - José Pintado
- Instituto de Investigaciones Marinas, CSIC, Vigo, Spain
| | - Mahasweta Saha
- Benthic Ecology, Helmholtz Center for Ocean Research, Kiel, Germany.,Marine Ecology and Biodiversity, Plymouth Marine Laboratory, Plymouth, United Kingdom
| | - Marc-André Selosse
- National Museum of Natural History, Département Systématique et Evolution, Paris, France.,Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Derek Skillings
- Philosophy Department, University of Pennsylvania, Philadelphia, United States of America
| | - Willem Stock
- Laboratory of Protistology & Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Shinichi Sunagawa
- Dept. of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH, Zürich, Switzerland
| | - Eve Toulza
- IHPE, Univ. de Montpellier, CNRS, IFREMER, UPDV, Perpignan, France
| | - Alexey Vorobev
- CEA - Institut de Biologie François Jacob, Genoscope, Evry, France
| | - Catherine Leblanc
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Fabrice Not
- Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
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41
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Haber M, Burgsdorf I, Handley KM, Rubin-Blum M, Steindler L. Genomic Insights Into the Lifestyles of Thaumarchaeota Inside Sponges. Front Microbiol 2021; 11:622824. [PMID: 33537022 PMCID: PMC7848895 DOI: 10.3389/fmicb.2020.622824] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022] Open
Abstract
Sponges are among the oldest metazoans and their success is partly due to their abundant and diverse microbial symbionts. They are one of the few animals that have Thaumarchaeota symbionts. Here we compare genomes of 11 Thaumarchaeota sponge symbionts, including three new genomes, to free-living ones. Like their free-living counterparts, sponge-associated Thaumarchaeota can oxidize ammonia, fix carbon, and produce several vitamins. Adaptions to life inside the sponge host include enrichment in transposases, toxin-antitoxin systems and restriction modifications systems, enrichments previously reported also from bacterial sponge symbionts. Most thaumarchaeal sponge symbionts lost the ability to synthesize rhamnose, which likely alters their cell surface and allows them to evade digestion by the host. All but one archaeal sponge symbiont encoded a high-affinity, branched-chain amino acid transporter system that was absent from the analyzed free-living thaumarchaeota suggesting a mixotrophic lifestyle for the sponge symbionts. Most of the other unique features found in sponge-associated Thaumarchaeota, were limited to only a few specific symbionts. These features included the presence of exopolyphosphatases and a glycine cleavage system found in the novel genomes. Thaumarchaeota have thus likely highly specific interactions with their sponge host, which is supported by the limited number of host sponge species to which each of these symbionts is restricted.
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Affiliation(s)
- Markus Haber
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, České Budějovice, Czechia
| | - Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Kim M. Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Maxim Rubin-Blum
- Israel Oceanographic and Limnological Research Institute, Haifa, Israel
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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42
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Oliveira BFR, Lopes IR, Canellas ALB, Muricy G, Dobson ADW, Laport MS. Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea. Microorganisms 2020; 8:microorganisms8121978. [PMID: 33322780 PMCID: PMC7764410 DOI: 10.3390/microorganisms8121978] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/12/2020] [Accepted: 11/25/2020] [Indexed: 01/28/2023] Open
Abstract
Marine sponges are excellent examples of invertebrate–microbe symbioses. In this holobiont, the partnership has elegantly evolved by either transmitting key microbial associates through the host germline and/or capturing microorganisms from the surrounding seawater. We report here on the prokaryotic microbiota during different developmental stages of Plakina cyanorosea and their surrounding environmental samples by a 16S rRNA metabarcoding approach. In comparison with their source adults, larvae housed slightly richer and more diverse microbial communities, which are structurally more related to the environmental microbiota. In addition to the thaumarchaeal Nitrosopumilus, parental sponges were broadly dominated by Alpha- and Gamma-proteobacteria, while the offspring were particularly enriched in the Vibrionales, Alteromonodales, Enterobacterales orders and the Clostridia and Bacteroidia classes. An enterobacterial operational taxonomic unit (OTU) was the dominant member of the strict core microbiota. The most abundant and unique OTUs were not significantly enriched amongst the microbiomes from host specimens included in the sponge microbiome project. In a wider context, Oscarella and Plakina are the sponge genera with higher divergence in their associated microbiota compared to their Homoscleromorpha counterparts. Our results indicate that P. cyanorosea is a low microbial abundance sponge (LMA), which appears to heavily depend on the horizontal transmission of its microbial partners that likely help the sponge host in the adaptation to its habitat.
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Affiliation(s)
- Bruno F. R. Oliveira
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
- School of Microbiology, University College Cork, T12 Y960 Cork, Ireland;
| | - Isabelle R. Lopes
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
| | - Anna L. B. Canellas
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
| | - Guilherme Muricy
- Laboratório de Biologia de Porifera, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro 20940040, Brazil;
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, T12 Y960 Cork, Ireland;
- Environmental Research Institute, University College Cork, T23 XE10 Cork, Ireland
| | - Marinella S. Laport
- Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; (B.F.R.O.); (I.R.L.); (A.L.B.C.)
- Correspondence:
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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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Zapién-Campos R, Sieber M, Traulsen A. Stochastic colonization of hosts with a finite lifespan can drive individual host microbes out of equilibrium. PLoS Comput Biol 2020; 16:e1008392. [PMID: 33137114 PMCID: PMC7660904 DOI: 10.1371/journal.pcbi.1008392] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 11/12/2020] [Accepted: 09/02/2020] [Indexed: 12/04/2022] Open
Abstract
Macroorganisms are inhabited by microbial communities that often change through the lifespan of an individual. One of the factors contributing to this change is colonization from the environment. The colonization of initially microbe-free hosts is particularly interesting, as their microbiome depends entirely on microbes of external origin. We present a mathematical model of this process with a particular emphasis on the effect of ecological drift and a finite host lifespan. Our results indicate the host lifespan becomes especially relevant for short-living organisms (e.g. Caenorhabditis elegans, Drosophila melanogaster, and Danio rerio). In this case, alternative microbiome states (often called enterotypes), the coexistence of microbe-free and colonized hosts, and a reduced probability of colonization can be observed in our model. These results unify multiple reported observations around colonization and suggest that no selective or deterministic drivers are necessary to explain them. Microbial communities are prevalent not only in the environment but also in hosts. Although the drivers of environmental microbiomes have been studied extensively, less is known about the drivers distinguishing a host environment. Recent experimental observations have highlighted the influence of ecological drift in hosts with short lifespan, including model organisms like C. elegans, D. melanogaster and D. rerio. We have developed a theoretical model to study the effect of a finite host lifespan on relevant observables of the microbiome, including the microbial load, probability of colonization of a microbial taxon, and distribution of microbiome composition in a host population. Although we focus on a case free of any selection, our results indicate the possible coexistence of hosts with alternative microbiome composition, and to a larger extent the coexistence of colonized and microbe-free hosts. A quantitative description is provided.
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Affiliation(s)
- Román Zapién-Campos
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Michael Sieber
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Arne Traulsen
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
- * E-mail:
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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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Host specificity of microbiome assembly and its fitness effects in phytoplankton. ISME JOURNAL 2020; 15:774-788. [PMID: 33097853 DOI: 10.1038/s41396-020-00812-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 12/21/2022]
Abstract
Insights into symbiosis between eukaryotic hosts and their microbiomes have shifted paradigms on what determines host fitness, ecology, and behavior. Questions remain regarding the roles of host versus environment in shaping microbiomes, and how microbiome composition affects host fitness. Using a model system in ecology, phytoplankton, we tested whether microbiomes are host-specific, confer fitness benefits that are host-specific, and remain conserved in time in their composition and fitness effects. We used an experimental approach in which hosts were cleaned of bacteria and then exposed to bacterial communities from natural environments to permit recruitment of microbiomes. We found that phytoplankton microbiomes consisted of a subset of taxa recruited from these natural environments. Microbiome recruitment was host-specific, with host species explaining more variation in microbiome composition than environment. While microbiome composition shifted and then stabilized over time, host specificity remained for dozens of generations. Microbiomes increased host fitness, but these fitness effects were host-specific for only two of the five species. The shifts in microbiome composition over time amplified fitness benefits to the hosts. Overall, this work solidifies the importance of host factors in shaping microbiomes and elucidates the temporal dynamics of microbiome compositional and fitness effects.
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Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts. ISME JOURNAL 2020; 15:503-519. [PMID: 33011742 DOI: 10.1038/s41396-020-00791-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 01/17/2023]
Abstract
The symbiosis between bacteria and sponges has arguably the longest evolutionary history for any extant metazoan lineage, yet little is known about bacterial evolution or adaptation in this process. An example of often dominant and widespread bacterial symbionts of sponges is a clade of uncultured and uncharacterised Proteobacteria. Here we set out to characterise this group using metagenomics, in-depth phylogenetic analyses, metatranscriptomics, and fluorescence in situ hybridisation microscopy. We obtained five metagenome-assembled-genomes (MAGs) from different sponge species that, together with a previously published MAG (AqS2), comprise two families within a new gammaproteobacterial order that we named UTethybacterales. Members of this order share a heterotrophic lifestyle but vary in their predicted ability to use various carbon, nitrogen and sulfur sources, including taurine, spermidine and dimethylsulfoniopropionate. The deep branching of the UTethybacterales within the Gammaproteobacteria and their almost exclusive presence in sponges suggests they have entered a symbiosis with their host relatively early in evolutionary time and have subsequently functionally radiated. This is reflected in quite distinct lifestyles of various species of UTethybacterales, most notably their diverse morphologies, predicted substrate preferences, and localisation within the sponge tissue. This study provides new insight into the evolution of metazoan-bacteria symbiosis.
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Abstract
Sequencing technologies have fuelled a rapid rise in descriptions of microbial communities associated with hosts, but what is often harder to ascertain is the evolutionary significance of these symbioses. Here, we review the role of vertical (VT), horizontal (HT), environmental acquisition and mixed modes of transmission (MMT), in the establishment of animal host–microbe associations. We then model four properties of gut microbiota proposed as key to promoting animal host–microbe relationships: modes of transmission, host reproductive mode, host mate choice and host fitness. We found that: (i) MMT led to the highest frequencies of host–microbe associations, and that some environmental acquisition or HT of microbes was required for persistent associations to form unless VT was perfect; (ii) host reproductive mode (sexual versus asexual) and host mate choice (for microbe carriers versus non-carriers) had little impact on the establishment of host–microbe associations; (iii) host mate choice did not itself lead to reproductive isolation, but could reinforce it; and (iv) changes in host fitness due to host–microbe associations had a minimal impact upon the formation of co-associations. When we introduced a second population, into which host–microbe carriers could disperse but in which environmental acquisition did not occur, highly efficient VT was required for host–microbe co-associations to persist. Our study reveals that transmission mode is of key importance in establishing host–microbe associations.
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Affiliation(s)
- Philip T Leftwich
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | | | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
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Koskella B, Bergelson J. The study of host-microbiome (co)evolution across levels of selection. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190604. [PMID: 32772660 DOI: 10.1098/rstb.2019.0604] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Microorganismal diversity can be explained in large part by selection imposed from both the abiotic and biotic environments, including-in the case of host-associated microbiomes-interactions with eukaryotes. As such, the diversity of host-associated microbiomes can be usefully studied across a variety of scales: within a single host over time, among host genotypes within a population, between populations and among host species. A plethora of recent studies across these scales and across diverse systems are: (i) exemplifying the importance of the host genetics in shaping microbiome composition; (ii) uncovering the role of the microbiome in shaping key host phenotypes; and (iii) highlighting the dynamic nature of the microbiome. They have also raised a critical question: do these complex associations fit within our existing understanding of evolution and coevolution, or do these often intimate and seemingly cross-generational interactions follow novel evolutionary rules from those previously identified? Herein, we describe the known importance of (co)evolution in host-microbiome systems, placing the existing data within extant frameworks that have been developed over decades of study, and ask whether there are unique properties of host-microbiome systems that require a paradigm shift. By examining when and how selection can act on the host and its microbiome as a unit (termed, the holobiont), we find that the existing conceptual framework, which focuses on individuals, as well as interactions among individuals and groups, is generally well suited for understanding (co)evolutionary change in these intimate assemblages. This article is part of the theme issue 'The role of the microbiome in host evolution'.
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Affiliation(s)
- Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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Figueiredo ART, Kramer J. Cooperation and Conflict Within the Microbiota and Their Effects On Animal Hosts. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00132] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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