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Stante M, Weiland-Bräuer N, von Hoyningen-Huene AJE, Schmitz RA. Marine bacteriophages disturb the associated microbiota of Aurelia aurita with a recoverable effect on host morphology. Front Microbiol 2024; 15:1356337. [PMID: 38533338 PMCID: PMC10964490 DOI: 10.3389/fmicb.2024.1356337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/21/2024] [Indexed: 03/28/2024] Open
Abstract
The concept of the metaorganism describes a multicellular host and its diverse microbial community, which form one biological unit with a combined genetic repertoire that significantly influences health and survival of the host. The present study delved into the emerging field of bacteriophage research within metaorganisms, focusing on the moon jellyfish Aurelia aurita as a model organism. The previously isolated Pseudomonas phage BSwM KMM1 and Citrobacter phages BSwM KMM2 - KMM4 demonstrated potent infectivity on bacteria present in the A. aurita-associated microbiota. In a host-fitness experiment, Baltic Sea subpopulation polyps were exposed to individual phages and a phage cocktail, monitoring polyp survival and morphology, as well as microbiome changes. The following effects were obtained. First, phage exposure in general led to recoverable malformations in polyps without affecting their survival. Second, analyses of the community structure, using 16S rRNA amplicon sequencing, revealed alterations in the associated microbial community in response to phage exposure. Third, the native microbiota is dominated by an uncultured likely novel Mycoplasma species, potentially specific to A. aurita. Notably, this main colonizer showed resilience through the recovery after initial declines, which aligned with abundance changes in Bacteroidota and Proteobacteria, suggesting a dynamic and adaptable microbial community. Overall, this study demonstrates the resilience of the A. aurita metaorganism facing phage-induced perturbations, emphasizing the importance of understanding host-phage interactions in metaorganism biology. These findings have implications for ecological adaptation and conservation in the rapidly changing marine environment, particularly regarding the regulation of blooming species and the health of marine ecosystems during ongoing environmental changes.
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Affiliation(s)
| | | | | | - Ruth Anne Schmitz
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
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2
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González-Aravena M, Perrois G, Font A, Cárdenas CA, Rondon R. Microbiome profile of the Antarctic clam Laternula elliptica. Braz J Microbiol 2024; 55:487-497. [PMID: 38157148 PMCID: PMC10920576 DOI: 10.1007/s42770-023-01200-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
The filter feeder clam Laternula elliptica is a key species in the Antarctic ecosystem. As a stenothermal benthic species, it has a poor capacity for adaptation to small temperature variations. Despite their ecological importance and sensitivity to climate change, studies on their microbiomes are lacking. The goal of this study was to characterize the bacterial communities of L. elliptica and the tissues variability of this microbiome to provide an initial insight of host-microbiota interactions. We investigated the diversity and taxonomic composition of bacterial communities of L. elliptica from five regions of the body using high-throughput 16S rRNA gene sequencing. The results showed that the microbiome of L. elliptica tended to differ from that of the surrounding seawater samples. However, there were no significant differences in the microbial composition between the body sites, and only two OTUs were present in all samples, being considered core microbiome (genus Moritella and Polaribacter). No significant differences were detected in diversity indexes among tissues (mean 626.85 for observed OTUs, 628.89 Chao1, 5.42 Shannon, and 0.87 Simpson). Rarefaction analysis revealed that most tissues reached a plateau of OTU number according to sample increase, with the exception of Siphon samples. Psychromonas and Psychrilyobacter were particularly abundant in L. elliptica whereas Fluviicola dominated seawater and siphons. Typical polar bacteria were Polaribacter, Shewanella, Colwellia, and Moritella. We detected the prevalence of pathogenic bacterial sequences, particularly in the family Arcobacteraceae, Pseudomonadaceae, and Mycoplasmataceae. The prokaryotic diversity was similar among tissues, as well as their taxonomic composition, suggesting a homogeneity of the microbiome along L. elliptica body. The Antarctic clam population can be used to monitor the impact of human activity in areas near Antarctic stations that discharge wastewater.
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Affiliation(s)
| | - Garance Perrois
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
- Tropical & Subtropical Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Alejandro Font
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
| | - César A Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | - Rodolfo Rondon
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile.
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3
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Ochoa-Sánchez M, Acuña Gomez EP, Ramírez-Fenández L, Eguiarte LE, Souza V. Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project. PeerJ 2023; 11:e15978. [PMID: 37810788 PMCID: PMC10557944 DOI: 10.7717/peerj.15978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/07/2023] [Indexed: 10/10/2023] Open
Abstract
Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.
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Affiliation(s)
- Manuel Ochoa-Sánchez
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Lia Ramírez-Fenández
- Facultad de Recursos Naturales Renovables, Universidad Arturo Prat, Iquique, Chile
- Centro de Desarrollo de Biotecnología Industrial y Bioproductos, Antofagasta, Chile
| | - Luis E. Eguiarte
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Valeria Souza
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
- Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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4
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Cevallos MA, Basanta MD, Bello-López E, Escobedo-Muñoz AS, González-Serrano FM, Nemec A, Romero-Contreras YJ, Serrano M, Rebollar EA. Genomic characterization of antifungal Acinetobacter bacteria isolated from the skin of the frogs Agalychnis callidryas and Craugastor fitzingeri. FEMS Microbiol Ecol 2022; 98:6775075. [PMID: 36288213 DOI: 10.1093/femsec/fiac126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/09/2022] [Accepted: 10/24/2022] [Indexed: 01/21/2023] Open
Abstract
Chytridiomycosis, a lethal fungal disease caused by Batrachochytrium dendrobatidis (Bd), is responsible for population declines and extinctions of amphibians worldwide. However, not all amphibian species are equally susceptible to the disease; some species persist in Bd enzootic regions with no population reductions. Recently, it has been shown that the amphibian skin microbiome plays a crucial role in the defense against Bd. Numerous bacterial isolates with the capacity to inhibit the growth of Batrachochytrium fungi have been isolated from the skin of amphibians. Here, we characterized eight Acinetobacter bacteria isolated from the frogs Agalychnis callidryas and Craugastor fitzingeri at the genomic level. A total of five isolates belonged to Acinetobacter pittii,Acinetobacter radioresistens, or Acinetobactermodestus, and three were not identified as any of the known species, suggesting they are members of new species. We showed that seven isolates inhibited the growth of Bd and that all eight isolates inhibited the growth of the phytopathogen fungus Botrytis cinerea. Finally, we identified the biosynthetic gene clusters that could be involved in the antifungal activity of these isolates. Our results suggest that the frog skin microbiome includes Acinetobacter isolates that are new to science and have broad antifungal functions, perhaps driven by distinct genetic mechanisms.
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Affiliation(s)
- M A Cevallos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - M D Basanta
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México.,Department of Biology, University of Nevada Reno, 1664 N Virgina St, Reno, NV 89557, United States
| | - E Bello-López
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - A S Escobedo-Muñoz
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - F M González-Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - A Nemec
- Laboratory of Bacterial Genetics, Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, 100 00 Prague 10, Czechia.,Department of Medical Microbiology, Second Faculty of Medicine, Charles University, and Motol University Hospital, V Úvalu 84, 150 06 Prague 5, Czechia
| | - Y J Romero-Contreras
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - M Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
| | - E A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca, Morelos, 62220, México
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5
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Lo Giudice A, Rizzo C. Bacteria Associated with Benthic Invertebrates from Extreme Marine Environments: Promising but Underexplored Sources of Biotechnologically Relevant Molecules. Mar Drugs 2022; 20:617. [PMID: 36286440 PMCID: PMC9605250 DOI: 10.3390/md20100617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 09/07/2024] Open
Abstract
Microbe-invertebrate associations, commonly occurring in nature, play a fundamental role in the life of symbionts, even in hostile habitats, assuming a key importance for both ecological and evolutionary studies and relevance in biotechnology. Extreme environments have emerged as a new frontier in natural product chemistry in the search for novel chemotypes of microbial origin with significant biological activities. However, to date, the main focus has been microbes from sediment and seawater, whereas those associated with biota have received significantly less attention. This review has been therefore conceived to summarize the main information on invertebrate-bacteria associations that are established in extreme marine environments. After a brief overview of currently known extreme marine environments and their main characteristics, a report on the associations between extremophilic microorganisms and macrobenthic organisms in such hostile habitats is provided. The second part of the review deals with biotechnologically relevant bioactive molecules involved in establishing and maintaining symbiotic associations.
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Affiliation(s)
- Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (CNR.ISP), Spianata S. Raineri 86, 98122 Messina, Italy
| | - Carmen Rizzo
- Institute of Polar Sciences, National Research Council (CNR.ISP), Spianata S. Raineri 86, 98122 Messina, Italy
- Stazione Zoologica Anton Dohrn, National Institute of Biology, Sicily Marine Centre, Department Ecosustainable Marine Biotechnology, Villa Pace, Contrada Porticatello 29, 98167 Messina, Italy
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6
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Discovery of an Antarctic Ascidian-Associated Uncultivated Verrucomicrobia with Antimelanoma Palmerolide Biosynthetic Potential. mSphere 2021; 6:e0075921. [PMID: 34851164 PMCID: PMC8636102 DOI: 10.1128/msphere.00759-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Antarctic marine ecosystem harbors a wealth of biological and chemical innovation that has risen in concert over millennia since the isolation of the continent and formation of the Antarctic circumpolar current. Scientific inquiry into the novelty of marine natural products produced by Antarctic benthic invertebrates led to the discovery of a bioactive macrolide, palmerolide A, that has specific activity against melanoma and holds considerable promise as an anticancer therapeutic. While this compound was isolated from the Antarctic ascidian Synoicum adareanum, its biosynthesis has since been hypothesized to be microbially mediated, given structural similarities to microbially produced hybrid nonribosomal peptide-polyketide macrolides. Here, we describe a metagenome-enabled investigation aimed at identifying the biosynthetic gene cluster (BGC) and palmerolide A-producing organism. A 74-kbp candidate BGC encoding the multimodular enzymatic machinery (hybrid type I-trans-AT polyketide synthase-nonribosomal peptide synthetase and tailoring functional domains) was identified and found to harbor key features predicted as necessary for palmerolide A biosynthesis. Surveys of ascidian microbiome samples targeting the candidate BGC revealed a high correlation between palmerolide gene targets and a single 16S rRNA gene variant (R = 0.83 to 0.99). Through repeated rounds of metagenome sequencing followed by binning contigs into metagenome-assembled genomes, we were able to retrieve a nearly complete genome (10 contigs) of the BGC-producing organism, a novel verrucomicrobium within the Opitutaceae family that we propose here as “Candidatus Synoicihabitans palmerolidicus.” The refined genome assembly harbors five highly similar BGC copies, along with structural and functional features that shed light on the host-associated nature of this unique bacterium. IMPORTANCE Palmerolide A has potential as a chemotherapeutic agent to target melanoma. We interrogated the microbiome of the Antarctic ascidian, Synoicum adareanum, using a cultivation-independent high-throughput sequencing and bioinformatic strategy. The metagenome-encoded biosynthetic machinery predicted to produce palmerolide A was found to be associated with the genome of a member of the S. adareanum core microbiome. Phylogenomic analysis suggests the organism represents a new deeply branching genus, “Candidatus Synoicihabitans palmerolidicus,” in the Opitutaceae family of the Verrucomicrobia phylum. The Ca. Synoicihabitans palmerolidicus 4.29-Mb genome encodes a repertoire of carbohydrate-utilizing and transport pathways, a chemotaxis system, flagellar biosynthetic capacity, and other regulatory elements enabling its ascidian-associated lifestyle. The palmerolide producer’s genome also contains five distinct copies of the large palmerolide biosynthetic gene cluster that may provide structural complexity of palmerolide variants.
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7
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Neu AT, Hughes IV, Allen EE, Roy K. Decade-scale stability and change in a marine bivalve microbiome. Mol Ecol 2021; 30:1237-1250. [PMID: 33432685 DOI: 10.1111/mec.15796] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/04/2020] [Accepted: 01/04/2021] [Indexed: 12/24/2022]
Abstract
Predicting how populations and communities of organisms will respond to anthropogenic change is of paramount concern in ecology today. For communities of microorganisms, however, these predictions remain challenging, primarily due to data limitations. Information about long-term dynamics of host-associated microbial communities, in particular, is lacking. In this study, we use well-preserved and freshly collected samples of soft tissue from a marine bivalve host, Donax gouldii, at a single site to quantify the diversity and composition of its microbiome over a decadal timescale. Site-level measurements of temperature, salinity and chlorophyll a allowed us to test how the microbiome of this species responded to two natural experiments: a seasonal increase in temperature and a phytoplankton bloom. Our results show that ethanol-preserved tissue can provide high-resolution information about temporal trends in compositions of host-associated microbial communities. Specifically, we found that the richness of amplicon sequence variants (ASVs) associated with D.gouldii did not change significantly over time despite increases in water temperature (+1.6°C due to seasonal change) and chlorophyll a concentration (more than ninefold). The phylogenetic composition of the communities, on the other hand, varied significantly between all collection years, with only six ASVs persisting over our sampling period. Overall, these results suggest that the diversity of microbial taxa associated with D.gouldii has remained stable over time and in response to seasonal environmental change over the course of more than a decade, but such stability is underlain by substantial turnover in the composition 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, CA, USA
| | - Ian V Hughes
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Eric E Allen
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.,Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kaustuv Roy
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
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8
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Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago , Antarctica. Mar Drugs 2020; 18:md18060298. [PMID: 32498449 PMCID: PMC7345734 DOI: 10.3390/md18060298] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 01/04/2023] Open
Abstract
Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64°46′ S, 64°03′ W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3–V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)—20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.
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9
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Rausch P, Rühlemann M, Hermes BM, Doms S, Dagan T, Dierking K, Domin H, Fraune S, von Frieling J, Hentschel U, Heinsen FA, Höppner M, Jahn MT, Jaspers C, Kissoyan KAB, Langfeldt D, Rehman A, Reusch TBH, Roeder T, Schmitz RA, Schulenburg H, Soluch R, Sommer F, Stukenbrock E, Weiland-Bräuer N, Rosenstiel P, Franke A, Bosch T, Baines JF. Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms. MICROBIOME 2019; 7:133. [PMID: 31521200 PMCID: PMC6744666 DOI: 10.1186/s40168-019-0743-1] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 08/23/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of multicellular organisms as "metaorganisms." The goal of the Collaborative Research Center "Origin and Function of Metaorganisms" is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants. METHODS In order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample. CONCLUSION While 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Overall, we recommend single- over multi-step amplification procedures, and although exceptions and trade-offs exist, the V3 V4 over the V1 V2 region of the 16S rRNA gene. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.
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Affiliation(s)
- Philipp Rausch
- Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen Ø, Denmark
| | - Malte Rühlemann
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Britt M. Hermes
- Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Shauni Doms
- Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Katja Dierking
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Hanna Domin
- Zoological Institute, Kiel University, Kiel, Germany
| | | | - Jakob von Frieling
- Molecular Physiology, Zoological Institute, Kiel University, Kiel, Germany
| | - Ute Hentschel
- Marine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Kiel University, Kiel, Germany
| | | | - Marc Höppner
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Martin T. Jahn
- Marine Ecology, Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Cornelia Jaspers
- Kiel University, Kiel, Germany
- Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Kohar Annie B. Kissoyan
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | | | - Ateequr Rehman
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Thorsten B. H. Reusch
- Kiel University, Kiel, Germany
- Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Thomas Roeder
- Molecular Physiology, Zoological Institute, Kiel University, Kiel, Germany
| | - Ruth A. Schmitz
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Ryszard Soluch
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Felix Sommer
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Eva Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Environmental Genomics, Botanical Institute, Kiel University, Kiel, Germany
| | | | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Thomas Bosch
- Zoological Institute, Kiel University, Kiel, Germany
| | - John F. Baines
- Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
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10
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Kellogg CA. Microbiomes of stony and soft deep-sea corals share rare core bacteria. MICROBIOME 2019; 7:90. [PMID: 31182168 PMCID: PMC6558771 DOI: 10.1186/s40168-019-0697-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 05/19/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Numerous studies have shown that bacteria form stable associations with host corals and have focused on identifying conserved "core microbiomes" of bacterial associates inferred to be serving key roles in the coral holobiont. Because studies tend to focus on only stony corals (order Scleractinia) or soft corals (order Alcyonacea), it is currently unknown if there are conserved bacteria that are shared by both. A meta-analysis was done of 16S rRNA amplicon data from multiple studies generated via identical methodology to allow direct comparisons of bacterial associates across seven deep-sea corals, including both stony and soft species: Anthothela grandiflora, Anthothela sp., Lateothela grandiflora, Lophelia pertusa, Paramuricea placomus, Primnoa pacifica, and Primnoa resedaeformis. RESULTS Twenty-three operational taxonomic units (OTUs) were consistently present in greater than 50% of the coral samples. Seven amplicon sequence variants (ASVs), five of which corresponded to a conserved OTU, were consistently present in greater than 30% of the coral samples including five or greater coral species. A majority of the conserved sequences had close matches with previously identified coral-associated bacteria. While known to dominate tropical and temperate coral microbiomes, Endozoicomonas were extremely rare or absent from these deep-sea corals. An Endozoicomonas OTU associated with Lo. pertusa in this study was most similar to those from shallow-water stony corals, while an OTU associated with Anthothela spp. was most similar to those from shallow-water gorgonians. CONCLUSIONS Bacterial sequences have been identified that are conserved at the level of class Anthozoa (i.e., found in both stony and soft corals, shallow and deep). These bacterial associates are therefore hypothesized to play important symbiotic roles and are highlighted for targeted future study. These conserved bacterial associates include taxa with the potential for nitrogen and sulfur cycling, detoxification, and hydrocarbon degradation. There is also some overlap with kit contaminants that need to be resolved. Rarely detected Endozoicomonas sequences are partitioned by whether the host is a stony coral or a soft coral, and the finer clustering pattern reflects the hosts' phylogeny.
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Affiliation(s)
- Christina A Kellogg
- St. Petersburg Coastal and Marine Science Center, US Geological Survey, 600 4th Street South, St. Petersburg, FL, 33701, USA.
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Russell MJ, Murray AE, Hand KP. The Possible Emergence of Life and Differentiation of a Shallow Biosphere on Irradiated Icy Worlds: The Example of Europa. ASTROBIOLOGY 2017; 17:1265-1273. [PMID: 29016193 PMCID: PMC5729856 DOI: 10.1089/ast.2016.1600] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 04/28/2017] [Indexed: 05/17/2023]
Abstract
Irradiated ice-covered ocean worlds with rocky mafic mantles may provide the conditions needed to drive the emergence and maintenance of life. Alkaline hydrothermal springs-relieving the geophysical, thermal, and chemical disequilibria between oceans and tidally stressed crusts-could generate inorganic barriers to the otherwise uncontrolled and kinetically disfavored oxidation of hydrothermal hydrogen and methane. Ionic gradients imposed across these inorganic barriers, comprising iron oxyhydroxides and sulfides, could drive the hydrogenation of carbon dioxide and the oxidation of methane through thermodynamically favorable metabolic pathways leading to early life-forms. In such chemostatic environments, fuels may eventually outweigh oxidants. Ice-covered oceans are primarily heated from below, creating convection that could transport putative microbial cells and cellular cooperatives upward to congregate beneath an ice shell, potentially giving rise to a highly focused shallow biosphere. It is here where electron acceptors, ultimately derived from the irradiated surface, could be delivered to such life-forms through exchange with the icy surface. Such zones would act as "electron disposal units" for the biosphere, and occupants might be transferred toward the surface by buoyant diapirs and even entrained into plumes. Key Words: Biofilms-Europa-Extraterrestrial life-Hydrothermal systems. Astrobiology 17, 1265-1273.
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Affiliation(s)
- Michael J. Russell
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Alison E. Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, Nevada
| | - Kevin P. Hand
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
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