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Ridley RS, Conrad RE, Lindner BG, Woo S, Konstantinidis KT. Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes. Sci Rep 2024; 14:8798. [PMID: 38627476 PMCID: PMC11021508 DOI: 10.1038/s41598-024-59279-x] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
Despite increasing efforts across various disciplines, the fate, transport, and impact of synthetic plastics on the environment and public health remain poorly understood. To better elucidate the microbial ecology of plastic waste and its potential for biotransformation, we conducted a large-scale analysis of all publicly available meta-omic studies investigating plastics (n = 27) in the environment. Notably, we observed low prevalence of known plastic degraders throughout most environments, except for substantial enrichment in riverine systems. This indicates rivers may be a highly promising environment for discovery of novel plastic bioremediation products. Ocean samples associated with degrading plastics showed clear differentiation from non-degrading polymers, showing enrichment of novel putative biodegrading taxa in the degraded samples. Regarding plastisphere pathogenicity, we observed significant enrichment of antimicrobial resistance genes on plastics but not of virulence factors. Additionally, we report a co-occurrence network analysis of 10 + million proteins associated with the plastisphere. This analysis revealed a localized sub-region enriched with known and putative plastizymes-these may be useful for deeper investigation of nature's ability to biodegrade man-made plastics. Finally, the combined data from our meta-analysis was used to construct a publicly available database, the Plastics Meta-omic Database (PMDB)-accessible at plasticmdb.org. These data should aid in the integrated exploration of the microbial plastisphere and facilitate research efforts investigating the fate and bioremediation potential of environmental plastic waste.
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Affiliation(s)
- Rodney S Ridley
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - Roth E Conrad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Blake G Lindner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Seongwook Woo
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Konstantinos T Konstantinidis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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Rodriguez-R LM, Conrad RE, Viver T, Feistel DJ, Lindner BG, Venter SN, Orellana LH, Amann R, Rossello-Mora R, Konstantinidis KT. An ANI gap within bacterial species that advances the definitions of intra-species units. mBio 2024; 15:e0269623. [PMID: 38085031 PMCID: PMC10790751 DOI: 10.1128/mbio.02696-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/03/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Bacterial strains and clonal complexes are two cornerstone concepts for microbiology that remain loosely defined, which confuses communication and research. Here we identify a natural gap in genome sequence comparisons among isolate genomes of all well-sequenced species that has gone unnoticed so far and could be used to more accurately and precisely define these and related concepts compared to current methods. These findings advance the molecular toolbox for accurately delineating and following the important units of diversity within prokaryotic species and thus should greatly facilitate future epidemiological and micro-diversity studies across clinical and environmental settings.
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Affiliation(s)
- Luis M. Rodriguez-R
- Department of Microbiology, and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Roth E. Conrad
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Tomeu Viver
- Department of Animal and Microbial Biodiversity, Marine Microbiology Group, Mediterranean Institutes for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Dorian J. Feistel
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Blake G. Lindner
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Stephanus N. Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Luis H. Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ramon Rossello-Mora
- Department of Animal and Microbial Biodiversity, Marine Microbiology Group, Mediterranean Institutes for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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3
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Viver T, Conrad RE, Rodriguez-R LM, Ramírez AS, Venter SN, Rocha-Cárdenas J, Llabrés M, Amann R, Konstantinidis KT, Rossello-Mora R. Towards estimating the number of strains that make up a natural bacterial population. Nat Commun 2024; 15:544. [PMID: 38228587 PMCID: PMC10791622 DOI: 10.1038/s41467-023-44622-z] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024] Open
Abstract
What a strain is and how many strains make up a natural bacterial population remain elusive concepts despite their apparent importance for assessing the role of intra-population diversity in disease emergence or response to environmental perturbations. To advance these concepts, we sequenced 138 randomly selected Salinibacter ruber isolates from two solar salterns and assessed these genomes against companion short-read metagenomes from the same samples. The distribution of genome-aggregate average nucleotide identity (ANI) values among these isolates revealed a bimodal distribution, with four-fold lower occurrence of values between 99.2% and 99.8% relative to ANI >99.8% or <99.2%, revealing a natural "gap" in the sequence space within species. Accordingly, we used this ANI gap to define genomovars and a higher ANI value of >99.99% and shared gene-content >99.0% to define strains. Using these thresholds and extrapolating from how many metagenomic reads each genomovar uniquely recruited, we estimated that -although our 138 isolates represented about 80% of the Sal. ruber population- the total population in one saltern pond is composed of 5,500 to 11,000 genomovars, the great majority of which appear to be rare in-situ. These data also revealed that the most frequently recovered isolate in lab media was often not the most abundant genomovar in-situ, suggesting that cultivation biases are significant, even in cases that cultivation procedures are thought to be robust. The methodology and ANI thresholds outlined here should represent a useful guide for future microdiversity surveys of additional microbial species.
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Affiliation(s)
- Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Roth E Conrad
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Luis M Rodriguez-R
- Department of Microbiology, and Digital Science Center (DiSC), Universität of Innsbruck, Innsbruck, Austria
| | - Ana S Ramírez
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jairo Rocha-Cárdenas
- Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain
| | - Mercè Llabrés
- Department of Mathematics and Computer Science, University of the Balearic Islands, Palma, 07122, Spain
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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Ramírez AS, Poveda JB, Dijkman R, Poveda C, Suárez-Pérez A, Rosales RS, Feberwee A, Szostak MP, Ressel L, Viver T, Calabuig P, Catania S, Gobbo F, Timofte D, Spergser J. Mycoplasma bradburyae sp. nov. isolated from the trachea of sea birds. Syst Appl Microbiol 2023; 46:126472. [PMID: 37839385 DOI: 10.1016/j.syapm.2023.126472] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/17/2023]
Abstract
In the search for mollicutes in wild birds, six Mycoplasma strains were isolated from tracheal swabs taken from four different species of seabirds. Four strains originated from three Yellow-legged gulls (Larus michahellis) and a Cory's shearwater (Calonectris borealis) from Spain, one from a South African Kelp gull (Larus dominicanus), and one from an Italian Black-headed gull (Chroicocephalus ridibundus). These Mycoplasma strains presented 99 % 16S rRNA gene sequence similarity values with Mycoplasma (M.) gallisepticum. Phylogenetic analyses of marker genes (16S rRNA gene and rpoB) confirmed the close relationship of the strains to M. gallisepticum and M. tullyi. The seabirds' strains grew well in modified Hayflick medium, and colonies showed typical fried egg morphology. They produced acid from glucose and mannose but did not hydrolyze arginine or urea. Transmission electron microscopy revealed a cell morphology characteristic of mycoplasmas, presenting spherical to flask-shaped cells with an attachment organelle. Gliding motility was also observed. Furthermore, serological tests, MALDI-ToF mass spectrometry and genomic studies demonstrated that the strains were different to any known Mycoplasma species, for which the name Mycoplasma bradburyae sp. nov. is proposed; the type strain is T158T (DSM 110708 = NCTC 14398).
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Affiliation(s)
- Ana S Ramírez
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - José B Poveda
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain.
| | - Remco Dijkman
- GD Animal Health, Arnsbergstraat 7, 7418 EZ, Deventer, the Netherlands
| | - Carlos Poveda
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Alejandro Suárez-Pérez
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Rubén S Rosales
- Unidad de Epidemiología y Medicina Preventiva, IUSA, Facultad de Veterinaria, Universidad de Las Palmas de Gran Canaria, C/Trasmontaña s/n, Arucas, 35413, Canary Islands, Spain
| | - Anneke Feberwee
- GD Animal Health, Arnsbergstraat 7, 7418 EZ, Deventer, the Netherlands
| | - Michael P Szostak
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Lorenzo Ressel
- University of Liverpool, Institute of Veterinary Science, Leahurst Campus, Neston CH64 7TE, UK
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), 07190, Esporles, Spain
| | - Pascual Calabuig
- Centro de Recuperación de Fauna Silvestre, Cabildo de Gran Canaria, Spain
| | - Salvatore Catania
- Mycoplasma Unit - SCT1-Verona, WOAH Reference Laboratory for Avian Mycoplasmosis, Istituto Zooprofilattico Sperimentale delle Venezie, 37060 Buttapietra (VR), Italy
| | - Federica Gobbo
- Mycoplasma Unit - SCT1-Verona, WOAH Reference Laboratory for Avian Mycoplasmosis, Istituto Zooprofilattico Sperimentale delle Venezie, 37060 Buttapietra (VR), Italy
| | - Dorina Timofte
- University of Liverpool, Institute of Veterinary Science, Leahurst Campus, Neston CH64 7TE, UK
| | - Joachim Spergser
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
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Peña-Montenegro TD, Kleindienst S, Allen AE, Eren AM, McCrow JP, Sánchez-Calderón JD, Arnold J, Joye SB. Species-specific responses of marine bacteria to environmental perturbation. ISME COMMUN 2023; 3:99. [PMID: 37736763 PMCID: PMC10516948 DOI: 10.1038/s43705-023-00310-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023]
Abstract
Environmental perturbations shape the structure and function of microbial communities. Oil spills are a major perturbation and resolving spills often requires active measures like dispersant application that can exacerbate the initial disturbance. Species-specific responses of microorganisms to oil and dispersant exposure during such perturbations remain largely unknown. We merged metatranscriptomic libraries with pangenomes to generate Core-Accessory Metatranscriptomes (CA-Metatranscriptomes) for two microbial hydrocarbon degraders that played important roles in the aftermath of the Deepwater Horizon oil spill. The Colwellia CA-Metatranscriptome illustrated pronounced dispersant-driven acceleration of core (~41%) and accessory gene (~59%) transcription, suggesting an opportunistic strategy. Marinobacter responded to oil exposure by expressing mainly accessory genes (~93%), suggesting an effective hydrocarbon-degrading lifestyle. The CA-Metatranscriptome approach offers a robust way to identify the underlying mechanisms of key microbial functions and highlights differences of specialist-vs-opportunistic responses to environmental disturbance.
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Affiliation(s)
- Tito D Peña-Montenegro
- Department of Marine Sciences, University of Georgia, 325 Sanford Dr., Athens, GA, 30602-3636, USA
- Institute of Bioinformatics, University of Georgia, 120 Green St., Athens, GA, 30602-7229, USA
- Grupo de Investigación y Desarrollo en Ciencias, Tecnología e Innovación (BioGRID), Sociedad de Doctores e Investigadores de Colombia (SoPhIC), Bogotá, Colombia
| | - Sara Kleindienst
- Department of Marine Sciences, University of Georgia, 325 Sanford Dr., Athens, GA, 30602-3636, USA
- Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), University of Stuttgart, Bandtäle 2, 70569, Stuttgart, Germany
| | - Andrew E Allen
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, 92037, USA
- Integrative Oceanography Division, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92037, USA
| | - A Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, University of Oldenburg, Oldenburg, 26129, Germany
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - John P McCrow
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Juan D Sánchez-Calderón
- Grupo de Investigación en Gestión Ecológica y Agroindustrial (GEA), Programa de Microbiología, Facultad de Ciencias Exactas y Naturales, Universidad Libre, Seccional Barranquilla, Barranquilla, Colombia
| | - Jonathan Arnold
- Institute of Bioinformatics, University of Georgia, 120 Green St., Athens, GA, 30602-7229, USA
- Department of Genetics, University of Georgia, 120 Green St., Athens, GA, 30602-7223, USA
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, 325 Sanford Dr., Athens, GA, 30602-3636, USA.
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Viver T, Conrad RE, Lucio M, Harir M, Urdiain M, Gago JF, Suárez-Suárez A, Bustos-Caparros E, Sanchez-Martinez R, Mayol E, Fassetta F, Pang J, Mădălin Gridan I, Venter S, Santos F, Baxter B, Llames ME, Cristea A, Banciu HL, Hedlund BP, Stott MB, Kämpfer P, Amann R, Schmitt-Kopplin P, Konstantinidis KT, Rossello-Mora R. Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov. Syst Appl Microbiol 2023; 46:126416. [PMID: 36965279 DOI: 10.1016/j.syapm.2023.126416] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023]
Abstract
Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31T, respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31T, respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.
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Affiliation(s)
- Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Roth E Conrad
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Marianna Lucio
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, 85764 Neuherberg, Germany
| | - Mourad Harir
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, 85764 Neuherberg, Germany; Chair of Analytical Food Chemistry, Technical University Munich, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Ana Suárez-Suárez
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Esteban Bustos-Caparros
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Rodrigo Sanchez-Martinez
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690, San Vicent del Raspeig, Alicante, Spain
| | - Eva Mayol
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690, San Vicent del Raspeig, Alicante, Spain
| | - Federico Fassetta
- Laboratorio de Ecología Acuática, Instituto Tecnológico Chascomús (INTECH)-CONICET-UNSAM, Escuela de Bio y Nanotecnologías -UNSAM, Buenos Aires, Argentina
| | - Jinfeng Pang
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154-4004, USA
| | - Ionuț Mădălin Gridan
- Doctoral School of Integrative Biology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Stephanus Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Fernando Santos
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690, San Vicent del Raspeig, Alicante, Spain
| | - Bonnie Baxter
- Great Salt Lake Institute, Westminster College, Salt Lake City, UT, 84105, USA
| | - María E Llames
- Laboratorio de Ecología Acuática, Instituto Tecnológico Chascomús (INTECH)-CONICET-UNSAM, Escuela de Bio y Nanotecnologías -UNSAM, Buenos Aires, Argentina
| | - Adorján Cristea
- Department of Taxonomy and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj‑Napoca, Romania
| | - Horia L Banciu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj‑Napoca, Romania; Emil G. Racoviță Institute, Babeș-Bolyai University, Cluj‑Napoca, Romania
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154-4004, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Peter Kämpfer
- Institute of Applied Microbiology (IFZ), Justus Liebig Universität Giessen, Giessen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, 85764 Neuherberg, Germany; Chair of Analytical Food Chemistry, Technical University Munich, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany
| | - Konstantinos T Konstantinidis
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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7
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Picazo DR, Werner A, Dagan T, Kupczok A. Pangenome evolution in environmentally transmitted symbionts of deep-sea mussels is governed by vertical inheritance. Genome Biol Evol 2022; 14:6613374. [PMID: 35731940 PMCID: PMC9260185 DOI: 10.1093/gbe/evac098] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial pangenomes vary across species; their size and structure are determined by genetic diversity within the population and by gene loss and horizontal gene transfer (HGT). Many bacteria are associated with eukaryotic hosts where the host colonization dynamics may impact bacterial genome evolution. Host-associated lifestyle has been recognized as a barrier to HGT in parentally transmitted bacteria. However, pangenome evolution of environmentally acquired symbionts remains understudied, often due to limitations in symbiont cultivation. Using high-resolution metagenomics, here we study pangenome evolution of two co-occurring endosymbionts inhabiting Bathymodiolus brooksi mussels from a single cold seep. The symbionts, sulfur-oxidizing (SOX) and methane-oxidizing (MOX) gamma-proteobacteria, are environmentally acquired at an early developmental stage and individual mussels may harbor multiple strains of each symbiont species. We found differences in the accessory gene content of both symbionts across individual mussels, which are reflected by differences in symbiont strain composition. Compared to core genes, accessory genes are enriched in genome plasticity functions. We found no evidence for recent horizontal gene transfer between both symbionts. A comparison between the symbiont pangenomes revealed that the MOX population is less diverged and contains fewer accessory genes, supporting that the MOX association with B. brooksi is more recent in comparison to that of SOX. Our results show that the pangenomes of both symbionts evolved mainly by vertical inheritance. We conclude that genome evolution of environmentally transmitted symbionts that associate with individual hosts over their lifetime is affected by a narrow symbiosis where the frequency of HGT is constrained..
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Affiliation(s)
- Devani Romero Picazo
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, Kiel, Germany
| | - Almut Werner
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, Kiel, Germany
| | - Tal Dagan
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, Kiel, Germany
| | - Anne Kupczok
- Genomic Microbiology Group, Institute of General Microbiology, Christian-Albrechts University, Kiel, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands
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8
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Gerhardt K, Ruiz-Perez CA, Rodriguez-R LM, Conrad RE, Konstantinidis KT. RecruitPlotEasy: An Advanced Read Recruitment Plot Tool for Assessing Metagenomic Population Abundance and Genetic Diversity. Front Bioinform 2022; 1:826701. [PMID: 36303791 PMCID: PMC9580866 DOI: 10.3389/fbinf.2021.826701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/28/2021] [Indexed: 11/14/2022] Open
Abstract
Mapping of short metagenomic (or metatranscriptomic) read data to reference isolate or single-cell genomes or metagenome-assembled genomes (MAGs) to assess microbial population relative abundance and/or structure represents an essential task of many studies across environmental and clinical settings. The filtering for the quality of the read match and assessment of read mapping results are frequently performed without visual aids or with the assistance of visualizations produced through ad-hoc, in-house approaches. Here, we introduce RecruitPlotEasy, a fully automated, user-friendly pipeline for these purposes that integrates statistical approaches to quantify intra-population sequence and gene-content diversity and identify co-occurring relative populations in the sample. Hence, RecruitPlotEasy should also greatly facilitate population genetics studies. RecruitPlotEasy is implemented in Python and R languages and is freely available open source software under the Artistic License 2.0 from https://github.com/KGerhardt/RecruitPlotEasy.
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Affiliation(s)
- Kenji Gerhardt
- School of Biological Sciences, Atlanta, GA, United States
- Center for Bioinformatics and Computational Genomics, Atlanta, GA, United States
| | - Carlos A. Ruiz-Perez
- School of Biological Sciences, Atlanta, GA, United States
- Center for Bioinformatics and Computational Genomics, Atlanta, GA, United States
| | - Luis M. Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | | | - Konstantinos T. Konstantinidis
- School of Biological Sciences, Atlanta, GA, United States
- Center for Bioinformatics and Computational Genomics, Atlanta, GA, United States
- Ocean Science & Engineering, Atlanta, GA, United States
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
- *Correspondence: Konstantinos T. Konstantinidis,
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