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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. Environ 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Díez-Vives C, Riesgo A. High compositional and functional similarity in the microbiome of deep-sea sponges. ISME J 2024; 18:wrad030. [PMID: 38365260 PMCID: PMC10837836 DOI: 10.1093/ismejo/wrad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 02/18/2024]
Abstract
Sponges largely depend on their symbiotic microbes for their nutrition, health, and survival. This is especially true in high microbial abundance (HMA) sponges, where filtration is usually deprecated in favor of a larger association with prokaryotic symbionts. Sponge-microbiome association is substantially less understood for deep-sea sponges than for shallow water species. This is most unfortunate, since HMA sponges can form massive sponge grounds in the deep sea, where they dominate the ecosystems, driving their biogeochemical cycles. Here, we assess the microbial transcriptional profile of three different deep-sea HMA sponges in four locations of the Cantabrian Sea and compared them to shallow water HMA and LMA (low microbial abundance) sponge species. Our results reveal that the sponge microbiome has converged in a fundamental metabolic role for deep-sea sponges, independent of taxonomic relationships or geographic location, which is shared in broad terms with shallow HMA species. We also observed a large number of redundant microbial members performing the same functions, likely providing stability to the sponge inner ecosystem. A comparison between the community composition of our deep-sea sponges and another 39 species of HMA sponges from deep-sea and shallow habitats, belonging to the same taxonomic orders, suggested strong homogeneity in microbial composition (i.e. weak species-specificity) in deep sea species, which contrasts with that observed in shallow water counterparts. This convergence in microbiome composition and functionality underscores the adaptation to an extremely restrictive environment with the aim of exploiting the available resources.
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Affiliation(s)
- Cristina Díez-Vives
- Department of Systems Biology, Centro Nacional de Biotecnología, c/ Darwin, 3, 28049 Madrid, Spain
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
| | - Ana Riesgo
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), c/José Gutiérrez Abascal 2, 28006 Madrid, Spain
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3
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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] [What about the content of this article? (0)] [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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4
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Taylor JA, Díez-Vives C, Nielsen S, Wemheuer B, Thomas T. Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts. Environ Microbiol 2022; 24:2299-2314. [PMID: 35229422 DOI: 10.1111/1462-2920.15962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/13/2022] [Accepted: 02/26/2022] [Indexed: 11/03/2022]
Abstract
The diversity and function of sponge-associated symbionts is now increasingly understood, however, we lack an understanding on how they dynamically behave to ensure holobiont stability in the face of environmental variation. Here we performed a metatransciptomics analysis of three microbial symbionts of the sponge Cymbastela concentrica in situ over 14 months and through differential gene expression and correlation analysis to environmental variables uncovered differences that speak to their metabolic activities and level of symbiotic and environmental interactions. The nitrite-oxidising Ca. Porinitrospira cymbastela maintained a seemingly stable metabolism, with the few differentially expressed genes related only to stress responses. The heterotrophic Ca. Porivivens multivorans displayed differential use of holobiont-derived compounds and respiration modes, while the ammonium-oxidising archaeon Ca. Nitrosopumilus cymbastelus differentially expressed genes related to phosphate metabolism and symbiosis effectors. One striking similarity between the symbionts was their similar variation in expression of stress-related genes. Our timeseries study showed that the microbial community of C. concentrica undertakes dynamic gene expression adjustments in response to the surroundings, tuned to deal with general stress and metabolic interactions between holobiont members. The success of these dynamic adjustments likely underpins the stability of the sponge holobiont and may provide resilience against environmental change. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jessica A Taylor
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Cristina Díez-Vives
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, Madrid, Spain
| | - Shaun Nielsen
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia
| | - Bernd Wemheuer
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
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Taylor JA, Díez-Vives C, Majzoub ME, Nielsen S, Thomas T. Stress response of the marine sponge Scopalina sp.. Can microbial community composition predict sponge disease? FEMS Microbiol Ecol 2021; 97:6310570. [PMID: 34180510 DOI: 10.1093/femsec/fiab095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
Disease has become an increasingly recognised problem in the marine environment, but our understanding of the factors that drive disease or our ability to predict its occurrence is limited. Marine sponges are known for their close associations with microorganisms, which are generally accepted to underpin sponge health and function. The aim of this study is to explore whether the microbial community composition of sponges can act as a predictor of disease occurrence under stressful environmental conditions. The development of a naturally occurring disease in the temperate sponge species Scopalina sp. was reproducibly recreated in a flow-through aquarium environment using increasing temperature stress. Throughout the experiments, four morphological health states were observed and described. Fingerprinting based on terminal restriction fragment length polymorphism of the bacterial community uncovered a statistically significant signature in healthy sponges prior to stress or apparent symptoms that correlated with the time it took for the disease to occur. This shows that the bacterial community composition of individual sponges can act as predictors of necrotic disease development. To the best of our knowledge, this is the first time a microbial signature of this nature has been reported in marine sponges and this finding can contribute to unravelling cause-effect pathways for stress-related dysbiosis and disease.
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Affiliation(s)
- Jessica A Taylor
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, NSW 2052, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Cristina Díez-Vives
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, NSW 2052, Australia.,Department of Life Sciences, The Natural History Museum, London, UK
| | - Marwan E Majzoub
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, NSW 2052, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Shaun Nielsen
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, NSW 2052, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, University of New South Wales, Sydney, NSW 2052, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Taboada S, Serra Silva A, Díez-Vives C, Neal L, Cristobo J, Ríos P, Hestetun JT, Clark B, Rossi ME, Junoy J, Navarro J, Riesgo A. Sleeping with the enemy: unravelling the symbiotic relationships between the scale worm Neopolynoe chondrocladiae (Annelida: Polynoidae) and its carnivorous sponge hosts. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
The North Atlantic deep-water polynoid worm Neopolynoe chondrocladiae is involved in an exceptional symbiotic relationship with two hosts: the carnivorous sponges Chondrocladia robertballardi and Chondrocladia virgata. While this is an obligate symbiotic relationship, its real nature is unclear. We used a multidisciplinary approach to narrow down the type of symbiotic relationship between symbiont and hosts. Molecular connectivity analyses using COI and 16S suggest that N. chondrocladiae has high potential for dispersal, connecting sites hundreds of kilometres apart, likely aided by oceanographic currents. Microbial analyses on different anatomical parts of five Chondrocladia species suggest that the presence of the worm in C. robertballardi does not affect the microbiome of the sponge. MicroCT analysis on N. chondrocladiae show that it has dorsally oriented parapodia, which might prevent the worm from getting trapped in the sponge. A faecal pellet recovered from the worm suggests that the polynoid feeds on the crustacean prey captured by the sponge, something corroborated by our stable isotope analysis. Light and confocal microscopy images suggest that N. chondrocladiae elytra produce bioluminescence. We propose that the worm might use bioluminescence as a lure for prey (increasing the food available for both the sponge and the polynoid) and thus fuelling a mutualistic relationship.
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Affiliation(s)
- Sergi Taboada
- Departamento de Ciencias de la Vida, Apdo. 20, Campus Universitario, Universidad de Alcalá, Alcalá de Henares, Spain
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, UK
- Departamento de Biología (Zoología), Universidad Autónoma de Madrid, Facultad de Ciencias, Cantoblanco, Madrid, Spain
| | - Ana Serra Silva
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, UK
- Division of Biosciences, University College London, Gower Street, London, UK
- School of Earth Sciences, University of Bristol, Queens Road, Bristol, UK
| | - Cristina Díez-Vives
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, UK
| | - Lenka Neal
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, UK
| | - Javier Cristobo
- Departamento de Ciencias de la Vida, Apdo. 20, Campus Universitario, Universidad de Alcalá, Alcalá de Henares, Spain
- Instituto Español de Oceanografía, Centro Oceanográfico de Gijón, C/ Príncipe de Asturias 70 bis, Gijón, Asturias, Spain
| | - Pilar Ríos
- Departamento de Ciencias de la Vida, Apdo. 20, Campus Universitario, Universidad de Alcalá, Alcalá de Henares, Spain
- Instituto Español de Oceanografía, Centro Oceanográfico de Santander, Promontorio San Martín s/n, Apdo. 240, Santander, Spain
| | - Jon Thomassen Hestetun
- NORCE Environment, NORCE Norwegian Research Centre, Nygårdsgaten 112 NO-5838 Bergen, Norway
| | - Brett Clark
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, UK
| | | | - Juan Junoy
- Departamento de Ciencias de la Vida, Apdo. 20, Campus Universitario, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Joan Navarro
- Instituto de Ciencias del Mar CSIC, Passeig Marítim de la Barceloneta 37–49, Barcelona, Spain
| | - Ana Riesgo
- Life Sciences Department, The Natural History Museum, Cromwell Road, London, UK
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7
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Abstract
AbstractBone-eating worms of the genus Osedax (Annelida, Siboglinidae) form unique holobionts (functional entity comprising host and associated microbiota), highly adapted to inhabit bone tissue of marine vertebrates. These gutless worms have developed nutritional symbioses housing intracellular, horizontally acquired, heterotrophic bacteria hypothesised to harness nutrients from organic compounds, sequestered within the bone. Despite previous efforts, critical mechanisms mediating activity and acquisition of diverse bacterial assemblages remain unclear. Using 16S rRNA amplicon sequencing, we performed detailed taxonomic and predicted functional analyses shedding light on the microbial communities of two shallow-water Osedax species (Osedax deceptionensis and Osedax ‘mediterranea’) from contrasting habitats (Antarctic and Mediterranean Sea), in two tissue types (roots and palps). Comparative assessments between host species revealed distinct microbial assemblages whilst, within host species and body tissue, relative symbiont frequencies retained high variability. We reported relatively high abundances of microbes previously classified as primary endosymbionts, Ribotype 1 (order Oceanospirillales), and diverse likely secondary epibionts warranting further exploration as recurrent Osedax associates. Surprisingly, O. ‘mediterranea’ exhibited relatively low abundance of Oceanospirillales, but increased abundance of other potentially hydrocarbon degrading bacteria from the family Alteromonadaceae. We hypothesise the presence of functionally similar, non-Oceanospirillales primary endosymbionts within O. ‘mediterranea’. Functional metagenomic profiling (using 16S rRNA sequences) predicted broad metabolic capabilities, encompassing relatively large abundances of genes associated with amino acid metabolism. Comparative analyses between host body tissue communities highlighted several genes potentially providing critical functions to the Osedax host or that confer adaptations for intracellular life, housed within bone embedded host root tissues.
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Kenny NJ, Francis WR, Rivera-Vicéns RE, Juravel K, de Mendoza A, Díez-Vives C, Lister R, Bezares-Calderón LA, Grombacher L, Roller M, Barlow LD, Camilli S, Ryan JF, Wörheide G, Hill AL, Riesgo A, Leys SP. Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri. Nat Commun 2020; 11:3676. [PMID: 32719321 PMCID: PMC7385117 DOI: 10.1038/s41467-020-17397-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/23/2020] [Indexed: 11/09/2022] Open
Abstract
The genomes of non-bilaterian metazoans are key to understanding the molecular basis of early animal evolution. However, a full comprehension of how animal-specific traits, such as nervous systems, arose is hindered by the scarcity and fragmented nature of genomes from key taxa, such as Porifera. Ephydatia muelleri is a freshwater sponge found across the northern hemisphere. Here, we present its 326 Mb genome, assembled to high contiguity (N50: 9.88 Mb) with 23 chromosomes on 24 scaffolds. Our analyses reveal a metazoan-typical genome architecture, with highly shared synteny across Metazoa, and suggest that adaptation to the extreme temperatures and conditions found in freshwater often involves gene duplication. The pancontinental distribution and ready laboratory culture of E. muelleri make this a highly practical model system which, with RNAseq, DNA methylation and bacterial amplicon data spanning its development and range, allows exploration of genomic changes both within sponges and in early animal evolution.
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Affiliation(s)
- Nathan J Kenny
- Department of Life Sciences, The Natural History Museum, Cromwell Rd, London, SW7 5BD, UK. .,Faculty of Health and Life Sciences, Oxford Brookes, Oxford, OX3 0BP, UK.
| | - Warren R Francis
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Ramón E Rivera-Vicéns
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany
| | - Ksenia Juravel
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany
| | - Alex de Mendoza
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia.,School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Cristina Díez-Vives
- Department of Life Sciences, The Natural History Museum, Cromwell Rd, London, SW7 5BD, UK
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Luis A Bezares-Calderón
- College of Life and Environmental Sciences, University of Exeter, Stocker Rd, Exeter, EX4 4QD, UK
| | - Lauren Grombacher
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Maša Roller
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Lael D Barlow
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Sara Camilli
- Department of Biology, Bates College, Lewiston, ME, 04240, USA
| | - Joseph F Ryan
- Whitney Lab for Marine Bioscience and the Department of Biology, University of Florida, St. Augustine, FL, 32080, USA
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany.,SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Str. 10, 80333, München, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, München, Germany
| | - April L Hill
- Department of Biology, Bates College, Lewiston, ME, 04240, USA
| | - Ana Riesgo
- Department of Life Sciences, The Natural History Museum, Cromwell Rd, London, SW7 5BD, UK
| | - Sally P Leys
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
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Georgieva MN, Taboada S, Riesgo A, Díez-Vives C, De Leo FC, Jeffreys RM, Copley JT, Little CTS, Ríos P, Cristobo J, Hestetun JT, Glover AG. Evidence of Vent-Adaptation in Sponges Living at the Periphery of Hydrothermal Vent Environments: Ecological and Evolutionary Implications. Front Microbiol 2020; 11:1636. [PMID: 32793148 PMCID: PMC7393317 DOI: 10.3389/fmicb.2020.01636] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/23/2020] [Indexed: 01/04/2023] Open
Abstract
The peripheral areas of deep-sea hydrothermal vents are often inhabited by an assemblage of animals distinct to those living close to vent chimneys. For many such taxa, it is considered that peak abundances in the vent periphery relate to the availability of hard substrate as well as the increased concentrations of organic matter generated at vents, compared to background areas. However, the peripheries of vents are less well-studied than the assemblages of vent-endemic taxa, and the mechanisms through which peripheral fauna may benefit from vent environments are generally unknown. Understanding this is crucial for evaluating the sphere of influence of hydrothermal vents and managing the impacts of future human activity within these environments, as well as offering insights into the processes of metazoan adaptation to vents. In this study, we explored the evolutionary histories, microbiomes and nutritional sources of two distantly-related sponge types living at the periphery of active hydrothermal vents in two different geological settings (Cladorhiza from the E2 vent site on the East Scotia Ridge, Southern Ocean, and Spinularia from the Endeavour vent site on the Juan de Fuca Ridge, North-East Pacific) to examine their relationship to nearby venting. Our results uncovered a close sister relationship between the majority of our E2 Cladorhiza specimens and the species Cladorhiza methanophila, known to harbor and obtain nutrition from methanotrophic symbionts at cold seeps. Our microbiome analyses demonstrated that both E2 Cladorhiza and Endeavour Spinularia sp. are associated with putative chemosynthetic Gammaproteobacteria, including Thioglobaceae (present in both sponge types) and Methylomonaceae (present in Spinularia sp.). These bacteria are closely related to chemoautotrophic symbionts of bathymodiolin mussels. Both vent-peripheral sponges demonstrate carbon and nitrogen isotopic signatures consistent with contributions to nutrition from chemosynthesis. This study expands the number of known associations between metazoans and potentially chemosynthetic Gammaproteobacteria, indicating that they can be incredibly widespread and also occur away from the immediate vicinity of chemosynthetic environments in the vent-periphery, where these sponges may be adapted to benefit from dispersed vent fluids.
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Affiliation(s)
| | - Sergi Taboada
- Life Sciences Department, Natural History Museum, London, United Kingdom
- Departamento de Biología (Zoología), Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Zoología y Antropología Física, Universidad de Alcalá, Madrid, Spain
| | - Ana Riesgo
- Life Sciences Department, Natural History Museum, London, United Kingdom
| | | | - Fabio C. De Leo
- Ocean Networks Canada, University of Victoria, Victoria, BC, Canada
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Rachel M. Jeffreys
- School of Environmental Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jonathan T. Copley
- School of Ocean and Earth Science, University of Southampton, Southampton, United Kingdom
| | - Crispin T. S. Little
- Life Sciences Department, Natural History Museum, London, United Kingdom
- School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Pilar Ríos
- Departamento de Zoología y Antropología Física, Universidad de Alcalá, Madrid, Spain
- Centro Oceanográfico de Santander, Instituto Español de Oceanografía, Santander, Spain
| | - Javier Cristobo
- Departamento de Zoología y Antropología Física, Universidad de Alcalá, Madrid, Spain
- Centro Oceanográfico de Gijón, Instituto Español de Oceanografía, Gijón, Spain
| | - Jon T. Hestetun
- NORCE Environment, Norwegian Research Centre (NORCE), Bergen, Norway
| | - Adrian G. Glover
- Life Sciences Department, Natural History Museum, London, United Kingdom
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10
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Díez-Vives C, Nielsen S, Sánchez P, Palenzuela O, Ferrera I, Sebastián M, Pedrós-Alió C, Gasol JM, Acinas SG. Delineation of ecologically distinct units of marine Bacteroidetes in the Northwestern Mediterranean Sea. Mol Ecol 2019; 28:2846-2859. [PMID: 30830717 DOI: 10.1111/mec.15068] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/13/2019] [Accepted: 02/27/2019] [Indexed: 01/18/2023]
Abstract
Bacteroidetes is one of the dominant phyla of ocean bacterioplankton, yet its diversity and population structure is poorly understood. To advance in the delineation of ecologically meaningful units within this group, we constructed near full-length 16S rRNA gene clone libraries from contrasting marine environments in the NW Mediterranean. Based on phylogeny and the associated ecological variables (depth and season), 24 different Bacteroidetes clades were delineated. By considering their relative abundance (from iTag amplicon sequencing studies), we described the distribution patterns of each of these clades, delimiting them as Ecologically Significant Taxonomic Units (ESTUs). Spatially, there was almost no overlap among ESTUs at different depths. In deep waters there was predominance of Owenweeksia, Leeuwenhoekiella, Muricauda-related genera, and some depth-associated ESTUs within the NS5 and NS2b marine clades. Seasonally, multi-annual dynamics of recurring ESTUs were present with dominance of some ESTUs within the NS4, NS5 and NS2b marine clades along most of the year, but with variable relative frequencies between months. A drastic change towards the predominance of Formosa-related ESTUs and one ESTU from the NS5 marine clade was typically present after the spring bloom. Even though there are no isolates available for these ESTUs to determine their physiology, correlation analyses identified the environmental preference of some of them. Overall, our results suggest that there is a high degree of niche specialisation within these closely related clades. This work constitutes a step forward in disentangling the ecology of marine Bacteroidetes, which are essential players in organic matter processing in the oceans.
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Affiliation(s)
- Cristina Díez-Vives
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Department of Life Sciences (Invertebrate Division), The Natural History Museum of London, London, UK
| | - Shaun Nielsen
- School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, New South Wales, Australia
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
| | - Oswaldo Palenzuela
- Department of Biology, Culture and Pathology of Marine Species, Instituto de Acuicultura Torre de la Sal, Ribera de Cabanes, Spain
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Instituto Español de Oceanografía, Centro Oceanográfico de Málaga, Fuengirola, Spain
| | - Marta Sebastián
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de las Palmas de Gran Canaria, ULPGC, Telde, Spain
| | - Carlos Pedrós-Alió
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, Madrid, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain
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11
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Díez-Vives C, Esteves AIS, Costa R, Nielsen S, Thomas T. Detecting signatures of a sponge-associated lifestyle in bacterial genomes. Environ Microbiol Rep 2018; 10:433-443. [PMID: 29707906 DOI: 10.1111/1758-2229.12655] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 04/23/2018] [Indexed: 06/08/2023]
Abstract
Sponges interact with diverse and rich communities of bacteria that are phylogenetically often distinct from their free-living counterparts. Recent genomics and metagenomic studies have indicated that bacterial sponge symbionts also have distinct functional features from free-living bacteria; however, it is unclear, if such genome-derived functional signatures are common and present in different symbiont taxa. We therefore compared here a large set of genomes from cultured (Pseudovibrio, Ruegeria and Aquimarina) and yet-uncultivated (Synechococcus) bacteria found in either sponge-associated or free-living sources. Our analysis revealed only very few genera-specific functions that could be correlated with a sponge-associated lifestyle. Using different sets of sponge-associated and free-living bacteria for each genus, we could however show that the functions identified as 'sponge-associated' are dependent on the reference comparison being made. Using simulation approaches, we show how this influences the robustness of identifying functional signatures and how evolutionary divergence and genomic adaptation can be distinguished. Our results highlight the future need for robust comparative analyses to define genomic signatures of symbiotic lifestyles, whether it is for symbionts of sponges or other host organisms.
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Affiliation(s)
- Cristina Díez-Vives
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Ana I S Esteves
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Rodrigo Costa
- Department of Bioengineering, Institute for Bioengineering and Biosciences (IBB), IST, Universidade de Lisboa, Lisbon, Portugal
| | - Shaun Nielsen
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
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12
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Lara E, Vaqué D, Sà EL, Boras JA, Gomes A, Borrull E, Díez-Vives C, Teira E, Pernice MC, Garcia FC, Forn I, Castillo YM, Peiró A, Salazar G, Morán XAG, Massana R, Catalá TS, Luna GM, Agustí S, Estrada M, Gasol JM, Duarte CM. Unveiling the role and life strategies of viruses from the surface to the dark ocean. Sci Adv 2017; 3:e1602565. [PMID: 28913418 PMCID: PMC5587022 DOI: 10.1126/sciadv.1602565] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 08/09/2017] [Indexed: 05/31/2023]
Abstract
Viruses are a key component of marine ecosystems, but the assessment of their global role in regulating microbial communities and the flux of carbon is precluded by a paucity of data, particularly in the deep ocean. We assessed patterns in viral abundance and production and the role of viral lysis as a driver of prokaryote mortality, from surface to bathypelagic layers, across the tropical and subtropical oceans. Viral abundance showed significant differences between oceans in the epipelagic and mesopelagic, but not in the bathypelagic, and decreased with depth, with an average power-law scaling exponent of -1.03 km-1 from an average of 7.76 × 106 viruses ml-1 in the epipelagic to 0.62 × 106 viruses ml-1 in the bathypelagic layer with an average integrated (0 to 4000 m) viral stock of about 0.004 to 0.044 g C m-2, half of which is found below 775 m. Lysogenic viral production was higher than lytic viral production in surface waters, whereas the opposite was found in the bathypelagic, where prokaryotic mortality due to viruses was estimated to be 60 times higher than grazing. Free viruses had turnover times of 0.1 days in the bathypelagic, revealing that viruses in the bathypelagic are highly dynamic. On the basis of the rates of lysed prokaryotic cells, we estimated that viruses release 145 Gt C year-1 in the global tropical and subtropical oceans. The active viral processes reported here demonstrate the importance of viruses in the production of dissolved organic carbon in the dark ocean, a major pathway in carbon cycling.
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Affiliation(s)
- Elena Lara
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
- Institute of Marine Sciences, National Research Council (CNR-ISMAR), Castello 2737/F Arsenale-Tesa 104, 30122 Venezia, Italy
| | - Dolors Vaqué
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Elisabet Laia Sà
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Julia A. Boras
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Ana Gomes
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Encarna Borrull
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Cristina Díez-Vives
- School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio-Innovation, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Eva Teira
- Departamento de Ecología y Biología Animal, Universidad de Vigo, University of Vigo, 36310 Vigo, Spain
| | - Massimo C. Pernice
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Francisca C. Garcia
- Centro Oceanográfico de Gijón/Xixón, Instituto Español de Oceanografía, Avenida Príncipe de Asturias, 70, 33212 Gijón/Xixón, Spain
| | - Irene Forn
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Yaiza M. Castillo
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Aida Peiró
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Guillem Salazar
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Xosé Anxelu G. Morán
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ramon Massana
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Teresa S. Catalá
- Instituto de Investigaciones Marinas, CSIC, Eduardo Cabello, 6, 36208 Vigo, Spain
- Departamento de Ecología and Instituto del Agua, Universidad de Granada, Avenida del Hospicio, S/N, 18010 Granada, Spain
| | | | - Susana Agustí
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Marta Estrada
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Josep M. Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consell Superior d’Investigacions Científiques (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain
| | - Carlos M. Duarte
- Red Sea Research Center, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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13
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Moitinho-Silva L, Díez-Vives C, Batani G, Esteves AIS, Jahn MT, Thomas T. Integrated metabolism in sponge-microbe symbiosis revealed by genome-centered metatranscriptomics. ISME J 2017; 11:1651-1666. [PMID: 28338677 PMCID: PMC5520145 DOI: 10.1038/ismej.2017.25] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/10/2017] [Accepted: 01/19/2017] [Indexed: 12/21/2022]
Abstract
Despite an increased understanding of functions in sponge microbiomes, the interactions among the symbionts and between symbionts and host are not well characterized. Here we reconstructed the metabolic interactions within the sponge Cymbastela concentrica microbiome in the context of functional features of symbiotic diatoms and the host. Three genome bins (CcPhy, CcNi and CcThau) were recovered from metagenomic data of C. concentrica, belonging to the proteobacterial family Phyllobacteriaceae, the Nitrospira genus and the thaumarchaeal order Nitrosopumilales. Gene expression was estimated by mapping C. concentrica metatranscriptomic reads. Our analyses indicated that CcPhy is heterotrophic, while CcNi and CcThau are chemolithoautotrophs. CcPhy expressed many transporters for the acquisition of dissolved organic compounds, likely available through the sponge's filtration activity and symbiotic carbon fixation. Coupled nitrification by CcThau and CcNi was reconstructed, supported by the observed close proximity of the cells in fluorescence in situ hybridization. CcPhy facultative anaerobic respiration and assimilation by diatoms may consume the resulting nitrate. Transcriptional analysis of diatom and sponge functions indicated that these organisms are likely sources of organic compounds, for example, creatine/creatinine and dissolved organic carbon, for other members of the symbiosis. Our results suggest that organic nitrogen compounds, for example, creatine, creatinine, urea and cyanate, fuel the nitrogen cycle within the sponge. This study provides an unprecedented view of the metabolic interactions within sponge-microbe symbiosis, bridging the gap between cell- and community-level knowledge.
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Affiliation(s)
- Lucas Moitinho-Silva
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Cristina Díez-Vives
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Giampiero Batani
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Ana IS Esteves
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
| | - Martin T Jahn
- Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Torsten Thomas
- Centre for Marine Bio-Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia
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14
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Díez-Vives C, Moitinho-Silva L, Nielsen S, Reynolds D, Thomas T. Expression of eukaryotic-like protein in the microbiome of sponges. Mol Ecol 2017; 26:1432-1451. [PMID: 28036141 DOI: 10.1111/mec.14003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/08/2016] [Accepted: 12/09/2016] [Indexed: 01/04/2023]
Abstract
Eukaryotic-like proteins (ELPs) are classes of proteins that are found in prokaryotes, but have a likely evolutionary origin in eukaryotes. ELPs have been postulated to mediate host-microbiome interactions. Recent work has discovered that prokaryotic symbionts of sponges contain abundant and diverse genes for ELPs, which could modulate interactions with their filter-feeding and phagocytic host. However, the extent to which these ELP genes are actually used and expressed by the symbionts is poorly understood. Here, we use metatranscriptomics to investigate ELP expression in the microbiomes of three different sponges (Cymbastella concentrica, Scopalina sp. and Tedania anhelens). We developed a workflow with optimized rRNA removal and in silico subtraction of host sequences to obtain a reliable symbiont metatranscriptome. This showed that between 1.3% and 2.3% of all symbiont transcripts contain genes for ELPs. Two classes of ELPs (cadherin and tetratricopeptide repeats) were abundantly expressed in the C. concentrica and Scopalina sp. microbiomes, while ankyrin repeat ELPs were predominant in the T. anhelens metatranscriptome. Comparison with transcripts that do not encode ELPs indicated a constitutive expression of ELPs across a range of bacterial and archaeal symbionts. Expressed ELPs also contained domains involved in protein secretion and/or were co-expressed with proteins involved in extracellular transport. This suggests these ELPs are likely exported, which could allow for direct interaction with the sponge. Our study shows that ELP genes in sponge symbionts represent actively expressed functions that could mediate molecular interaction between symbiosis partners.
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Affiliation(s)
- C Díez-Vives
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| | - L Moitinho-Silva
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| | - S Nielsen
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| | - D Reynolds
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
| | - T Thomas
- Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia
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15
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Salazar G, Cornejo-Castillo FM, Borrull E, Díez-Vives C, Lara E, Vaqué D, Arrieta JM, Duarte CM, Gasol JM, Acinas SG. Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes. Mol Ecol 2015; 24:5692-706. [DOI: 10.1111/mec.13419] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/29/2015] [Accepted: 10/08/2015] [Indexed: 01/24/2023]
Affiliation(s)
- Guillem Salazar
- Department of Marine Biology and Oceanography; Institut de Ciències del Mar, CSIC; Pg Marítim de la Barceloneta 37-49 E08003 Barcelona Catalunya Spain
| | - Francisco M. Cornejo-Castillo
- Department of Marine Biology and Oceanography; Institut de Ciències del Mar, CSIC; Pg Marítim de la Barceloneta 37-49 E08003 Barcelona Catalunya Spain
| | - Encarna Borrull
- Department of Marine Biology and Oceanography; Institut de Ciències del Mar, CSIC; Pg Marítim de la Barceloneta 37-49 E08003 Barcelona Catalunya Spain
| | - Cristina Díez-Vives
- School of Biotechnology and Biomolecular Sciences; Centre for Marine Bio-Innovation; The University of New South Wales; Sydney NSW 2052 Australia
| | - Elena Lara
- Institute of Marine Sciences (CNR-ISMAR); National Research Council; Castello 2737/F Arsenale-Tesa 104 30122 Venezia Italy
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography; Institut de Ciències del Mar, CSIC; Pg Marítim de la Barceloneta 37-49 E08003 Barcelona Catalunya Spain
| | - Jesús M. Arrieta
- King Abdullah University of Science and Technology (KAUST); Red Sea Research Center (RSRC); Thuwal 23955-6900 Saudi Arabia
| | - Carlos M. Duarte
- King Abdullah University of Science and Technology (KAUST); Red Sea Research Center (RSRC); Thuwal 23955-6900 Saudi Arabia
| | - Josep M. Gasol
- Department of Marine Biology and Oceanography; Institut de Ciències del Mar, CSIC; Pg Marítim de la Barceloneta 37-49 E08003 Barcelona Catalunya Spain
| | - Silvia G. Acinas
- Department of Marine Biology and Oceanography; Institut de Ciències del Mar, CSIC; Pg Marítim de la Barceloneta 37-49 E08003 Barcelona Catalunya Spain
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16
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Acinas SG, Ferrera I, Sarmento H, Díez-Vives C, Forn I, Ruiz-González C, Cornejo-Castillo FM, Salazar G, Gasol JM. Validation of a new catalysed reporter deposition-fluorescence in situ hybridization probe for the accurate quantification of marine Bacteroidetes populations. Environ Microbiol 2014; 17:3557-69. [PMID: 24890225 DOI: 10.1111/1462-2920.12517] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 05/18/2014] [Indexed: 11/29/2022]
Abstract
Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH) is a powerful approach to quantify bacterial taxa. In this study, we compare the performance of the widely used Bacteroidetes CF319a probe with the new CF968 probe. In silico analyses and tests with isolates demonstrate that CF319a hybridizes with non-Bacteroidetes sequences from the Rhodobacteraceae and Alteromonadaceae families. We test the probes' accuracy in 37 globally distributed marine samples and over two consecutive years at the Blanes Bay Microbial Observatory (NW Mediterranean). We also compared the CARD-FISH data with the Bacteroidetes 16S rRNA gene sequences retrieved from 27 marine metagenomes from the TARA Oceans expedition. We find no significant differences in abundances between both approaches, although CF319a targeted some unspecific sequences and both probes displayed different abundances of specific Bacteroidetes phylotypes. Our results demonstrate that quantitative estimations by using both probes are significantly different in certain oceanographic regions (Mediterranean Sea, Red Sea and Arabian Sea) and that CF968 shows seasonality within marine Bacteroidetes, notably large differences between summer and winter that is overlooked by CF319a. We propose CF968 as an alternative to CF319a for targeting the whole Bacteroidetes phylum since it has better coverage, greater specificity and overall better quantifies marine Bacteroidetes.
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Affiliation(s)
- Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain
| | - Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain
| | - Hugo Sarmento
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain.,Department of Hydrobiology, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | - Cristina Díez-Vives
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain
| | - Irene Forn
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain
| | - Clara Ruiz-González
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain.,Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Francisco M Cornejo-Castillo
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain
| | - Guillem Salazar
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain
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17
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Abstract
Microbes are known to form intricate and intimate relationships with most animal and plant taxa. Microbe--host symbiotic associations are poorly explored in comparison with other species interaction networks. The current paradigm on symbiosis research stems from species-poor systems where pairwise and reciprocally specialized interactions between a single microbe and a single host that coevolve are the norm. These symbioses involving just a few species are fascinating in their own right, but more diverse and complex host-associated microbial communities are increasingly found, with new emerging questions that require new paradigms and approaches. Here we adopt an intermediate complexity approach to study the specificity, phylogenetic community structure, and temporal variability of the subset of the most abundant bacteria associated with different sponge host species with diverse eco-evolutionary characteristics. We do so by using a monthly resolved annual temporal series of host-associated and free-living bacteria. Bacteria are very abundant and diverse within marine sponges, and these symbiotic interactions are hypothesized to have a very ancient origin. We show that host-bacteria reciprocal specialization depends on the temporal scale and level of taxonomic aggregation considered. Sponge hosts with similar eco-evolutionary characteristics (e.g., volume of tissue corresponding to microbes, water filtering rates, and microbial transmission type) have similar bacterial phylogenetic community structure when looking at interactions aggregated over time. In general, sponge hosts hypothesized to form more intricate relationships with bacteria show a remarkably persistent bacterial community over time. Other hosts, however, show a large turnover similar to that observed for free-living bacterioplankton. Our study highlights the importance of exploring temporal variability in host--microbe interaction networks if we aim to determine how specific and persistent these poorly explored but extremely common interactions are.
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Affiliation(s)
- Johannes R Björk
- Instituto de Ciencias del Mar, Agencia Estatal Consejo Superior de Investigaciones Científicas, Passeig Maritim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - C Díez-Vives
- Instituto de Ciencias del Mar, Agencia Estatal Consejo Superior de Investigaciones Científicas, Passeig Maritim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Rafel Coma
- Centre d'Estudis Avançats de Blanes, Consejo Superior de Investigaciones Científicas (CEAB-CSIC), Accés Cala Sant Francesc 14, 17300 Blanes, Spain
| | - Marta Ribes
- Instituto de Ciencias del Mar, Agencia Estatal Consejo Superior de Investigaciones Científicas, Passeig Maritim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - José M Montoya
- Instituto de Ciencias del Mar, Agencia Estatal Consejo Superior de Investigaciones Científicas, Passeig Maritim de la Barceloneta 37-49, 08003, Barcelona, Spain
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Díez-Vives C, Gasol JM, Acinas SG. Spatial and temporal variability among marine Bacteroidetes populations in the NW Mediterranean Sea. Syst Appl Microbiol 2013; 37:68-78. [PMID: 24188570 DOI: 10.1016/j.syapm.2013.08.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 07/25/2013] [Accepted: 08/21/2013] [Indexed: 11/29/2022]
Abstract
The abundance and structure of Bacteroidetes populations at diverse temporal and spatial scales were investigated in the Northwestern Mediterranean Sea. At a temporal scale, their relative abundance exhibited a marked seasonality, since it was higher in spring and decreased in winter. Similarly, Bacteroidetes community structure encompassed three main groups (winter, spring and summer-fall), which mimicked global bacterioplankton seasonality. At the spatial scale, relative abundances were similar in all surface samples along an inshore-offshore transect, but they decreased with depth. Analysis of the community structure identified four markedly different groups mostly related to different depths. Interestingly, seasonal changes in abundance and community structure were not synchronized. Furthermore, richness was higher when Bacteroidetes were less abundant. The variability of Bacteroidetes contributions to community structure in the temporal and spatial scales was correlated with different environmental factors: day length was the most important factor at the temporal scale, and salinity at the spatial scale. The community composition in terms of phylotypes changed significantly over time and along the depth gradients, but season or depth-specific phylogenetic clusters were not identified. Delineation of coherent Bacteroidetes sub-clusters should help to uncover higher resolution patterns within Bacteroidetes, and explore associations with environmental and biological variables.
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Affiliation(s)
- Cristina Díez-Vives
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), ES-08003 Barcelona, Catalunya, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), ES-08003 Barcelona, Catalunya, Spain
| | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), ES-08003 Barcelona, Catalunya, Spain.
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Díez-Vives C, Gasol JM, Acinas SG. Evaluation of marine bacteroidetes-specific primers for microbial diversity and dynamics studies. Microb Ecol 2012; 64:1047-1055. [PMID: 22805741 DOI: 10.1007/s00248-012-0087-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Accepted: 06/04/2012] [Indexed: 06/01/2023]
Abstract
Assumptions on the matching specificity of group-specific bacterial primers may bias the interpretation of environmental microbial studies. As available sequence data continue growing, the performance of primers and probes needs to be reevaluated. Here, we present an evaluation of several commonly used and one newly designed Bacteroidetes-specific primer (CF418). First, we revised the in silico primer coverage and specificity with the current SILVA and RDP databases. We found minor differences with previous studies, which could be explained by the chosen databases, taxonomies, and matching criteria. We selected eight commonly used Bacteroidetes primers and tested them with a collection of assorted marine bacterial isolates. We also used the denaturing gradient gel electrophoresis (DGGE) approach in environmental samples to evaluate their ability to yield clear and diverse band patterns corresponding to Bacteroidetes phylotypes. Among the primers tested, CF968R did not provide satisfactory results in DGGE, although it exhibited the highest in silico coverage for Flavobacteria. Primers CFB560 and CFB555 presented undesirable features, such as requiring nested protocols or presence of degeneracies. Finally, the new primer CF418 and primer CF319a were used to explore the Bacteroidetes dynamics throughout a 1-year cycle in Mediterranean coastal waters (Blanes Bay Microbial Observatory). Both primers provided clear and diverse banding patterns, but the low specificity of CF319a was evidenced by 83.3 % of the bands sequenced corresponding to nontarget taxa. The satisfactory DGGE banding patterns and the wide diversity of sequences retrieved from DGGE bands with primer CF418 prove it to be a valuable alternative for the study of Bacteroidetes communities, recovering a wide range of phylotypes within the group.
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Affiliation(s)
- Cristina Díez-Vives
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas, ES-08003, Barcelona, Catalunya, Spain
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Díez-Vives C, Gay M, García-Matas S, Comellas F, Carrascal M, Abian J, Ortega-Aznar A, Cristòfol R, Sanfeliu C. Proteomic study of neuron and astrocyte cultures from senescence-accelerated mouse SAMP8 reveals degenerative changes. J Neurochem 2009; 111:945-55. [PMID: 19735447 DOI: 10.1111/j.1471-4159.2009.06374.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Senescence-accelerated prone (SAMP) strain 8 mice suffer an earlier development of cognitive age-related pathologies and a shorter life span than conventional mice. Protein alterations in astrocytes, in addition to those in neurons, may contribute to neurodegenerative damage. We applied proteomics techniques to study cell-specific early markers of brain aging-related degeneration in SAMP8. The two-dimensional protein expression patterns of the SAMP8 neuron and astrocyte cultures were compared with those obtained from senescence-accelerated resistant mouse strain 1 cultures. Differentially expressed spots were identified by matrix-assisted laser desorption/ionization-time of flight peptide map fingerprinting and database search. Proteins belonged to cell pathways of energy metabolism, biosynthesis, cell transduction and signaling, stress response, and the maintenance of cytoskeletal functions. Most of the changes were cell type specific. However, there was a general increase in cell transduction, signaling, and stress-related proteins and a decrease in cytoskeletal proteins. In addition, neurons showed an increased expression of proteins involved in biosynthetic pathways. A number of the protein alterations have been previously reported in the brain tissue proteome of SAMP8, aged brain or Alzheimer's disease brain. Alterations in neuron and astrocyte proteoma indicated that both cell types are involved in the brain degenerative changes of SAMP8 mice. However, network analysis suggests that neuronal changes are more complex and have a greater influence.
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Affiliation(s)
- Cristina Díez-Vives
- Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona, CSIC-IDIBAPS, Barcelona, Spain
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García-Matas S, Gutierrez-Cuesta J, Coto-Montes A, Rubio-Acero R, Díez-Vives C, Camins A, Pallàs M, Sanfeliu C, Cristòfol R. Dysfunction of astrocytes in senescence-accelerated mice SAMP8 reduces their neuroprotective capacity. Aging Cell 2008; 7:630-40. [PMID: 18616637 DOI: 10.1111/j.1474-9726.2008.00410.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Early onset increases in oxidative stress and tau pathology are present in the brain of senescence-accelerated mice prone (SAMP8). Astrocytes play an essential role, both in determining the brain's susceptibility to oxidative damage and in protecting neurons. In this study, we examine changes in tau phosphorylation, oxidative stress and glutamate uptake in primary cultures of cortical astrocytes from neonatal SAMP8 mice and senescence-accelerated-resistant mice (SAMR1). We demonstrated an enhancement of abnormally phosphorylated tau in Ser(199) and Ser(396) in SAMP8 astrocytes compared with that of SAMR1 control mice. Gsk3beta and Cdk5 kinase activity, which regulate tau phosphorylation, was also increased in SAMP8 astrocytes. Inhibition of Gsk3beta by lithium or Cdk5 by roscovitine reduced tau phosphorylation at Ser(396). Moreover, we detected an increase in radical superoxide generation, which may be responsible for the corresponding increase in lipoperoxidation and protein oxidation. We also observed a reduced mitochondrial membrane potential in SAMP8 mouse astrocytes. Glutamate uptake in astrocytes is a critical neuroprotective mechanism. SAMP8 astrocytes showed a decreased glutamate uptake compared with those of SAMR1 controls. Interestingly, survival of SAMP8 or SAMR1 neurons cocultured with SAMP8 astrocytes was significantly reduced. Our results indicate that alterations in astrocyte cultures from SAMP8 mice are similar to those detected in whole brains of SAMP8 mice at 1-5 months. Moreover, our findings suggest that this in vitro preparation is suitable for studying the molecular and cellular processes underlying early aging in this murine model. In addition, our study supports the contention that astrocytes play a key role in neurodegeneration during the aging process.
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Affiliation(s)
- Silvia García-Matas
- Department of Pharmacology and Toxicology, Institut d'Investigacions Biomèdiques de Barcelona, CSIC-IDIBAPS, Barcelona, Spain
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