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Arboleda-Baena C, Pareja CB, Pla I, Logares R, De la Iglesia R, Navarrete SA. Hidden interactions in the intertidal rocky shore: variation in pedal mucus microbiota among marine grazers that feed on epilithic biofilm communities. PeerJ 2022; 10:e13642. [PMID: 36172502 PMCID: PMC9512015 DOI: 10.7717/peerj.13642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 06/07/2022] [Indexed: 01/17/2023] Open
Abstract
In marine ecosystems, most invertebrates possess diverse microbiomes on their external surfaces, such as those found in the pedal mucus of grazing gastropods and chitons that aids displacement on different surfaces. The microbes are then transported around and placed in contact with free-living microbial communities of micro and other macro-organisms, potentially exchanging species and homogenizing microbial composition and structure among grazer hosts. Here, we characterize the microbiota of the pedal mucus of five distantly related mollusk grazers, quantify differences in microbial community structure, mucus protein and carbohydrate content, and, through a simple laboratory experiment, assess their effects on integrated measures of biofilm abundance. Over 665 Amplicon Sequence Variants (ASVs) were found across grazers, with significant differences in abundance and composition among grazer species and epilithic biofilms. The pulmonate limpet Siphonaria lessonii and the periwinkle Echinolittorina peruviana shared similar microbiota. The microbiota of the chiton Chiton granosus, keyhole limpet Fissurella crassa, and scurrinid limpet Scurria araucana differed markedly from one another, and form those of the pulmonate limpet and periwinkle. Flavobacteriaceae (Bacteroidia) and Colwelliaceae (Gammaproteobacteria) were the most common among microbial taxa. Microbial strict specialists were found in only one grazer species. The pedal mucus pH was similar among grazers, but carbohydrate and protein concentrations differed significantly. Yet, differences in mucus composition were not reflected in microbial community structure. Only the pedal mucus of F. crassa and S. lessonii negatively affected the abundance of photosynthetic microorganisms in the biofilm, demonstrating the specificity of the pedal mucus effects on biofilm communities. Thus, the pedal mucus microbiota are distinct among grazer hosts and can affect and interact non-trophically with the epilithic biofilms on which grazers feed, potentially leading to microbial community coalescence mediated by grazer movement. Further studies are needed to unravel the myriad of non-trophic interactions and their reciprocal impacts between macro- and microbial communities.
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Affiliation(s)
- Clara Arboleda-Baena
- Estación Costera de Investigaciones Marinas and Center for Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, El Tabo, Chile,Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago de Chile, Región Metropolitana, Chile
| | - Claudia Belén Pareja
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago de Chile, Región Metropolitana, Chile
| | - Isadora Pla
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago de Chile, Región Metropolitana, Chile
| | - Ramiro Logares
- Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalonia, Spain
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago de Chile, Región Metropolitana, Chile,Marine Energy Research & Innovation Center (MERIC), Santiago de Chile, Chile
| | - Sergio Andrés Navarrete
- Estación Costera de Investigaciones Marinas and Center for Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, El Tabo, Chile,Marine Energy Research & Innovation Center (MERIC), Santiago de Chile, Chile,Centro Basal COPAS-COASTAL, Universidad de Concepción
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Divergence together with microbes: A comparative study of the associated microbiomes in the closely related Littorina species. PLoS One 2021; 16:e0260792. [PMID: 34932575 PMCID: PMC8691637 DOI: 10.1371/journal.pone.0260792] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022] Open
Abstract
Any multicellular organism during its life is involved in relatively stable interactions with microorganisms. The organism and its microbiome make up a holobiont, possessing a unique set of characteristics and evolving as a whole system. This study aimed to evaluate the degree of the conservativeness of microbiomes associated with intertidal gastropods. We studied the composition and the geographic and phylogenetic variability of the gut and body surface microbiomes of five closely related sympatric Littorina (Neritrema) spp. and a more distant species, L. littorea, from the sister subgenus Littorina (Littorina). Although snail-associated microbiomes included many lineages (207–603), they were dominated by a small number of OTUs of the genera Psychromonas, Vibrio, and Psychrilyobacter. The geographic variability was greater than the interspecific differences at the same collection site. While the microbiomes of the six Littorina spp. did not differ at the high taxonomic level, the OTU composition differed between groups of cryptic species and subgenera. A few species-specific OTUs were detected within the collection sites; notably, such OTUs never dominated microbiomes. We conclude that the composition of the high-rank taxa of the associated microbiome (“scaffolding enterotype”) is more evolutionarily conserved than the composition of the low-rank individual OTUs, which may be site- and / or species-specific.
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Impact of Marine Aquaculture on the Microbiome Associated with Nearby Holobionts: The Case of Patella caerulea Living in Proximity of Sea Bream Aquaculture Cages. Microorganisms 2021; 9:microorganisms9020455. [PMID: 33671759 PMCID: PMC7927081 DOI: 10.3390/microorganisms9020455] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 01/04/2023] Open
Abstract
Aquaculture plays a major role in the coastal economy of the Mediterranean Sea. This raises the issue of the impact of fish cages on the surrounding environment. Here, we explore the impact of aquaculture on the composition of the digestive gland microbiome of a representative locally dwelling wild holobiont, the grazer gastropod Patella caerulea, at an aquaculture facility located in Southern Sicily, Italy. The microbiome was assessed in individuals collected on sea bream aquaculture cages and on a rocky coastal tract located about 1.2 km from the cages, as the control site. Patella caerulea microbiome variations were explained in the broad marine metacommunity context, assessing the water and sediment microbiome composition at both sites, and characterizing the microbiome associated with the farmed sea bream. The P. caerulea digestive gland microbiome at the aquaculture site was characterized by a lower diversity, the loss of microorganisms sensitive to heavy metal contamination, and by the acquisition of fish pathogens and parasites. However, we also observed possible adaptive responses of the P. caerulea digestive gland microbiome at the aquaculture site, including the acquisition of putative bacteria able to deal with metal and sulfide accumulation, highlighting the inherent microbiome potential to drive the host acclimation to stressful conditions.
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Enteromorpha prolifera Diet Drives Intestinal Microbiome Composition in Siganus oramin. Curr Microbiol 2020; 78:229-237. [PMID: 33034768 DOI: 10.1007/s00284-020-02218-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 09/17/2020] [Indexed: 12/14/2022]
Abstract
Enteromorpha prolifera (E. prolifera) contains complex sulfated polysaccharides that are resistant to biological degradation. Most organisms cannot digest biomass of E. prolifera, except Siganus oramin (S. oramin). This study was conducted to identify the bacteria in the intestine of S. oramin facilitating the digestion of E. prolifera polysaccharides (EPP). Metagenomic sequencing analysis of the S. oramin intestinal microbiota revealed that E. prolifera diet increased the number of Firmicutes, replacing Proteobacteria to be the dominant bacteria. The proportion of Firmicutes increased from 38.8 to 58.6%, with Bacteroidetes increasing nearly fivefold from 5 to 23.7%. 16S rDNA high-throughput sequencing showed that EPP-induced Bacteroidetes increased significantly in the intestinal flora of S. oramin cultivated in vitro. Metatranscriptome analysis showed that EPP induced more transferase, polysaccharide hydrolase, glycoside hydrolase, and esterases expressed in vitro, and most of them were taxonomically annotated to Bacteroidetes. Compared with the aggregation of GH family genes in metagenomic sequencing analysis in vivo, EPP induced more CBM32, GH2, GT2, GT30, and GH30 families gene expression in vitro. In general, We found that the bacteria in intestinal tract of S. oramin responsible for digestion of E. prolifera were Firmicutes and Bacteroidetes, while Bacteroidetes was the dominant bacteria involved in EPP degradation in vitro cultures. Compared with in vivo experiments, only GH family genes were mostly involved, we detected a more complete and complex EPP degradation pathway in vitro. The results may benefit the further study of biodegradation of E. prolifera and has potential implications for the utilization of E. prolifera for biotechnology.
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Structure and function of the digestive system in molluscs. Cell Tissue Res 2019; 377:475-503. [DOI: 10.1007/s00441-019-03085-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/26/2019] [Indexed: 02/06/2023]
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Neu AT, Allen EE, Roy K. Diversity and composition of intertidal gastropod microbiomes across a major marine biogeographic boundary. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:434-447. [PMID: 30834681 DOI: 10.1111/1758-2229.12743] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/02/2019] [Indexed: 06/09/2023]
Abstract
Marine biogeographic boundaries act as barriers to dispersal for many animal species, thereby creating distinctive faunas on either side. However, how such boundaries affect the distributions of microbial taxa remains poorly known. To test whether biogeographic boundaries influence the diversity and composition of host-associated microbiota, we analysed the microbiomes of three species of common intertidal gastropods at two sites separated by the biogeographic boundary at Point Conception (PtC), CA, using 16S rRNA gene sequencing. Our results show that each host species shows microbiome compositional specificity, even across PtC, and that alpha diversity does not change significantly across this boundary for any of the gastropod hosts. However, for two of the host species, beta diversity differs significantly across PtC, indicating that there may be multiple levels of organization of the marine gastropod microbiome. Overall, our results suggest that while biogeographic boundaries do not constrain the distribution of a core set of microbes associated with each host species, they can play a role in structuring the transient portion of the microbiome.
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Affiliation(s)
- Alexander T Neu
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Eric E Allen
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Kaustuv Roy
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
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Aires T, Serebryakova A, Viard F, Serrão EA, Engelen AH. Acidification increases abundances of Vibrionales and Planctomycetia associated to a seaweed-grazer system: potential consequences for disease and prey digestion efficiency. PeerJ 2018; 6:e4377. [PMID: 29610702 PMCID: PMC5880178 DOI: 10.7717/peerj.4377] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/26/2018] [Indexed: 01/28/2023] Open
Abstract
Ocean acidification significantly affects marine organisms in several ways, with complex interactions. Seaweeds might benefit from rising CO2 through increased photosynthesis and carbon acquisition, with subsequent higher growth rates. However, changes in seaweed chemistry due to increased CO2 may change the nutritional quality of tissue for grazers. In addition, organisms live in close association with a diverse microbiota, which can also be influenced by environmental changes, with feedback effects. As gut microbiomes are often linked to diet, changes in seaweed characteristics and associated microbiome can affect the gut microbiome of the grazer, with possible fitness consequences. In this study, we experimentally investigated the effects of acidification on the microbiome of the invasive brown seaweed Sargassum muticum and a native isopod consumer Synisoma nadejda. Both were exposed to ambient CO2 conditions (380 ppm, pH 8.16) and an acidification treatment (1,000 ppm, pH 7.86) for three weeks. Microbiome diversity and composition were determined using high-throughput sequencing of the variable regions V5-7 of 16S rRNA. We anticipated that as a result of acidification, the seaweed-associated bacterial community would change, leading to further changes in the gut microbiome of grazers. However, no significant effects of elevated CO2 on the overall bacterial community structure and composition were revealed in the seaweed. In contrast, significant changes were observed in the bacterial community of the grazer gut. Although the bacterial community of S. muticum as whole did not change, Oceanospirillales and Vibrionales (mainly Pseudoalteromonas) significantly increased their abundance in acidified conditions. The former, which uses organic matter compounds as its main source, may have opportunistically taken advantage of the possible increase of the C/N ratio in the seaweed under acidified conditions. Pseudoalteromonas, commonly associated to diseased seaweeds, suggesting that acidification may facilitate opportunistic/pathogenic bacteria. In the gut of S. nadejda, the bacterial genus Planctomycetia increased abundance under elevated CO2. This shift might be associated to changes in food (S. muticum) quality under acidification. Planctomycetia are slow-acting decomposers of algal polymers that could be providing the isopod with an elevated algal digestion and availability of inorganic compounds to compensate the shifted C/N ratio under acidification in their food. In conclusion, our results indicate that even after only three weeks of acidified conditions, bacterial communities associated to ungrazed seaweed and to an isopod grazer show specific, differential shifts in associated bacterial community. These have potential consequences for seaweed health (as shown in corals) and isopod food digestion. The observed changes in the gut microbiome of the grazer seem to reflect changes in the seaweed chemistry rather than its microbial composition.
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Affiliation(s)
- Tania Aires
- Center for Marine Sciences (CCMAR), CIMAR, University of Algarve, Campus de Gambelas, Faro, Portugal
| | - Alexandra Serebryakova
- Center for Marine Sciences (CCMAR), CIMAR, University of Algarve, Campus de Gambelas, Faro, Portugal.,Sorbonne Université, CNRS, Lab Adaptation and Diversity in Marine Environments (UMR 7144 CNRS SU), Station Biologique de Roscoff, Roscoff, France
| | - Frédérique Viard
- Sorbonne Université, CNRS, Lab Adaptation and Diversity in Marine Environments (UMR 7144 CNRS SU), Station Biologique de Roscoff, Roscoff, France.,CNRS, UMR 7144, Divco Team, Station Biologique de Roscoff, Roscoff, France
| | - Ester A Serrão
- Center for Marine Sciences (CCMAR), CIMAR, University of Algarve, Campus de Gambelas, Faro, Portugal
| | - Aschwin H Engelen
- Center for Marine Sciences (CCMAR), CIMAR, University of Algarve, Campus de Gambelas, Faro, Portugal
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Gobet A, Mest L, Perennou M, Dittami SM, Caralp C, Coulombet C, Huchette S, Roussel S, Michel G, Leblanc C. Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore. MICROBIOME 2018; 6:60. [PMID: 29587830 PMCID: PMC5870069 DOI: 10.1186/s40168-018-0430-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/23/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND Holobionts have a digestive microbiota with catabolic abilities allowing the degradation of complex dietary compounds for the host. In terrestrial herbivores, the digestive microbiota is known to degrade complex polysaccharides from land plants while in marine herbivores, the digestive microbiota is poorly characterized. Most of the latter are generalists and consume red, green, and brown macroalgae, three distinct lineages characterized by a specific composition in complex polysaccharides, which represent half of their biomass. Subsequently, each macroalga features a specific epiphytic microbiota, and the digestive microbiota of marine herbivores is expected to vary with a monospecific algal diet. We investigated the effect of four monospecific diets (Palmaria palmata, Ulva lactuca, Saccharina latissima, Laminaria digitata) on the composition and specificity of the digestive microbiota of a generalist marine herbivore, the abalone, farmed in a temperate coastal area over a year. The microbiota from the abalone digestive gland was sampled every 2 months and explored using metabarcoding. RESULTS Diversity and multivariate analyses showed that patterns of the microbiota were significantly linked to seasonal variations of contextual parameters but not directly to a specific algal diet. Three core genera: Psychrilyobacter, Mycoplasma, and Vibrio constantly dominated the microbiota in the abalone digestive gland. Additionally, a less abundant and diet-specific core microbiota featured genera representing aerobic primary degraders of algal polysaccharides. CONCLUSIONS This study highlights the establishment of a persistent core microbiota in the digestive gland of the abalone since its juvenile state and the presence of a less abundant and diet-specific core community. While composed of different microbial taxa compared to terrestrial herbivores, the digestive gland constitutes a particular niche in the abalone holobiont, where bacteria (i) may cooperate to degrade algal polysaccharides to products assimilable by the host or (ii) may have acquired these functions through gene transfer from the aerobic algal microbiota.
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Affiliation(s)
- Angélique Gobet
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff Cedex, France
| | - Laëtitia Mest
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff Cedex, France
| | - Morgan Perennou
- Sorbonne Universités, UPMC Université Paris 06, CNRS, FR2424, Genomer, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff Cedex, France
| | - Simon M Dittami
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff Cedex, France
| | | | | | | | | | - Gurvan Michel
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff Cedex, France
| | - Catherine Leblanc
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff Cedex, France
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Ngangbam AK, Baten A, Waters DLE, Whalan S, Benkendorff K. Characterization of Bacterial Communities Associated with the Tyrian Purple Producing Gland in a Marine Gastropod. PLoS One 2015; 10:e0140725. [PMID: 26488885 PMCID: PMC4619447 DOI: 10.1371/journal.pone.0140725] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/28/2015] [Indexed: 11/19/2022] Open
Abstract
Dicathais orbita is a marine mollusc recognised for the production of anticancer compounds that are precursors to Tyrian purple. This study aimed to assess the diversity and identity of bacteria associated with the Tyrian purple producing hypobranchial gland, in comparison with foot tissue, using a high-throughput sequencing approach. Taxonomic and phylogenetic analysis of variable region V1-V3 of 16S rRNA bacterial gene amplicons in QIIME and MEGAN were carried out. This analysis revealed a highly diverse bacterial assemblage associated with the hypobranchial gland and foot tissues of D. orbita. The dominant bacterial phylum in the 16S rRNA bacterial profiling data set was Proteobacteria followed by Bacteroidetes, Tenericutes and Spirochaetes. In comparison to the foot, the hypobranchial gland had significantly lower bacterial diversity and a different community composition, based on taxonomic assignment at the genus level. A higher abundance of indole producing Vibrio spp. and the presence of bacteria with brominating capabilities in the hypobranchial gland suggest bacteria have a potential role in biosynthesis of Tyrian purple in D. orbita.
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Affiliation(s)
- Ajit Kumar Ngangbam
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia
| | - Abdul Baten
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Daniel L. E. Waters
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Steve Whalan
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia
| | - Kirsten Benkendorff
- Marine Ecology Research Centre, School of Environment, Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia
- * E-mail:
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