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Zhang Y, Xue B, Mao Y, Chen X, Yan W, Wang Y, Wang Y, Liu L, Yu J, Zhang X, Chao S, Topp E, Zheng W, Zhang T. High-throughput single-cell sequencing of activated sludge microbiome. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2025; 23:100493. [PMID: 39430728 PMCID: PMC11490935 DOI: 10.1016/j.ese.2024.100493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 09/11/2024] [Accepted: 09/11/2024] [Indexed: 10/22/2024]
Abstract
Wastewater treatment plants (WWTPs) represent one of biotechnology's largest and most critical applications, playing a pivotal role in environmental protection and public health. In WWTPs, activated sludge (AS) plays a major role in removing contaminants and pathogens from wastewater. While metagenomics has advanced our understanding of microbial communities, it still faces challenges in revealing the genomic heterogeneity of cells, uncovering the microbial dark matter, and establishing precise links between genetic elements and their host cells as a bulk method. These issues could be largely resolved by single-cell sequencing, which can offer unprecedented resolution to show the unique genetic information. Here we show the high-throughput single-cell sequencing to the AS microbiome. The single-amplified genomes (SAGs) of 15,110 individual cells were clustered into 2,454 SAG bins. We find that 27.5% of the genomes in the AS microbial community represent potential novel species, highlighting the presence of microbial dark matter. Furthermore, we identified 1,137 antibiotic resistance genes (ARGs), 10,450 plasmid fragments, and 1,343 phage contigs, with shared plasmid and phage groups broadly distributed among hosts, indicating a high frequency of horizontal gene transfer (HGT) within the AS microbiome. Complementary analysis using 1,529 metagenome-assembled genomes from the AS samples allowed for the taxonomic classification of 98 SAG bins, which were previously unclassified. Our study establishes the feasibility of single-cell sequencing in characterizing the AS microbiome, providing novel insights into its ecological dynamics, and deepening our understanding of HGT processes, particularly those involving ARGs. Additionally, this valuable tool could monitor the distribution, spread, and pathogenic hosts of ARGs both within AS environments and between AS and other environments, which will ultimately contribute to developing a health risk evaluation system for diverse environments within a One Health framework.
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Affiliation(s)
- Yulin Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| | - Bingjie Xue
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
- School of Public Health, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518071, Guangdong, China
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, 518071, Guangdong, China
| | - Xi Chen
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| | - Weifu Yan
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| | - Yanren Wang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| | - Jiale Yu
- MobiDrop (Zhejiang) Company Limited, Jiaxing, 314000, Zhejiang, China
| | - Xiaojin Zhang
- MobiDrop (Zhejiang) Company Limited, Jiaxing, 314000, Zhejiang, China
| | - Shan Chao
- MobiDrop (Zhejiang) Company Limited, Jiaxing, 314000, Zhejiang, China
| | - Edward Topp
- Agroecology Research unit, Bourgogne Franche-Comté Research Centre, National Research Institute for Agriculture, Food and the Environment, 35000, France
| | - Wenshan Zheng
- MobiDrop (Zhejiang) Company Limited, Jiaxing, 314000, Zhejiang, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
- School of Public Health, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
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2
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Mateo-Cáceres V, Redrejo-Rodríguez M. Pipolins are bimodular platforms that maintain a reservoir of defense systems exchangeable with various bacterial genetic mobile elements. Nucleic Acids Res 2024; 52:12498-12516. [PMID: 39404074 PMCID: PMC11551731 DOI: 10.1093/nar/gkae891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 09/23/2024] [Accepted: 09/26/2024] [Indexed: 11/12/2024] Open
Abstract
Defense genes gather in diverse types of genomic islands in bacteria and provide immunity against viruses and other genetic mobile elements. Here, we disclose pipolins, previously found in diverse bacterial phyla and encoding a primer-independent PolB, as a new category of widespread defense islands. The analysis of the occurrence and structure of pipolins revealed that they are commonly integrative elements flanked by direct repeats in Gammaproteobacteria genomes, mainly Escherichia, Vibrio or Aeromonas, often taking up known mobile elements integration hotspots. Remarkably, integrase dynamics correlates with alternative integration spots and enables diverse lifestyles, from integrative to mobilizable and plasmid pipolins, such as in members of the genera Limosilactobacillus, Pseudosulfitobacter or Staphylococcus. Pipolins harbor a minimal core and a large cargo module enriched for defense factors. In addition, analysis of the weighted gene repertoire relatedness revealed that many of these defense factors are actively exchanged with other mobile elements. These findings indicate pipolins and, potentially other defense islands, act as orthogonal reservoirs of defense genes, potentially transferable to immune autonomous MGEs, suggesting complementary exchange mechanisms for defense genes in bacterial populations.
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Affiliation(s)
- Víctor Mateo-Cáceres
- Department of Biochemistry, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Sols-Morreale (CSIC-UAM), Madrid, Spain
| | - Modesto Redrejo-Rodríguez
- Department of Biochemistry, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Sols-Morreale (CSIC-UAM), Madrid, Spain
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3
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Duchin Rapp Y, Lipsman V, Yuda L, Kublanov IV, Matsliyah D, Segev E. Algal exudates promote conjugation in marine Roseobacters. mBio 2024; 15:e0106224. [PMID: 39189747 PMCID: PMC11481893 DOI: 10.1128/mbio.01062-24] [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: 04/07/2024] [Accepted: 07/22/2024] [Indexed: 08/28/2024] Open
Abstract
Horizontal gene transfer (HGT) is a pivotal mechanism driving bacterial evolution, conferring adaptability within dynamic marine ecosystems. Among HGT mechanisms, conjugation mediated by type IV secretion systems (T4SSs) plays a central role in the ecological success of marine bacteria. However, the conditions promoting conjugation events in the marine environment are not well-understood. Roseobacters, abundant marine bacteria commonly associated with algae, possess a multitude of T4SSs. Many Roseobacters are heterotrophic bacteria that rely on algal secreted compounds to support their growth. These compounds attract bacteria, facilitating colonization and attachment to algal cells. Algae and their metabolites bring bacteria into close proximity, potentially promoting bacterial HGT. Investigation across various Roseobacters revealed that algal exudates indeed enhance plasmid transfer through conjugation. While algal exudates do not influence the transcription of bacterial conjugative machinery genes, they promote bacterial attachment, potentially stabilizing proximity and facilitating HGT. Notably, under conditions where attachment is less advantageous, the impact of algal exudates on conjugation is reduced. These findings suggest that algae enhance bacterial conjugation primarily by fostering attachment and highlight the importance of studying bacterial HGT within the context of algal-bacterial interactions. IMPORTANCE This study explores how algal-bacterial interactions influence horizontal gene transfer (HGT) among marine bacteria. HGT, a key driver of bacterial evolution, is facilitated by conjugation mediated by type IV secretion systems (T4SSs). Through investigating Roseobacters, abundant marine bacteria often found to be associated with algae, the study reveals that algal exudates enhance plasmid transfer via conjugation. This enhancement is attributed to the promotion of bacterial attachment by algal compounds, emphasizing the role of algal-bacterial interactions in shaping genetic exchange within dynamic marine ecosystems. Understanding these mechanisms is crucial for elucidating bacterial adaptability and evolution in the marine environment.
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Affiliation(s)
- Yemima Duchin Rapp
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Valeria Lipsman
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lilach Yuda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ilya V. Kublanov
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dor Matsliyah
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Einat Segev
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
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4
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Flamholz ZN, Li C, Kelly L. Improving viral annotation with artificial intelligence. mBio 2024; 15:e0320623. [PMID: 39230289 PMCID: PMC11481560 DOI: 10.1128/mbio.03206-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024] Open
Abstract
Viruses of bacteria, "phages," are fundamental, poorly understood components of microbial community structure and function. Additionally, their dependence on hosts for replication positions phages as unique sensors of ecosystem features and environmental pressures. High-throughput sequencing approaches have begun to give us access to the diversity and range of phage populations in complex microbial community samples, and metagenomics is currently the primary tool with which we study phage populations. The study of phages by metagenomic sequencing, however, is fundamentally limited by viral diversity, which results in the vast majority of viral genomes and metagenome-annotated genomes lacking annotation. To harness bacteriophages for applications in human and environmental health and disease, we need new methods to organize and annotate viral sequence diversity. We recently demonstrated that methods that leverage self-supervised representation learning can supplement statistical sequence representations for remote viral protein homology detection in the ocean virome and propose that consideration of the functional content of viral sequences allows for the identification of similarity in otherwise sequence-diverse viruses and viral-like elements for biological discovery. In this review, we describe the potential and pitfalls of large language models for viral annotation. We describe the need for new approaches to annotate viral sequences in metagenomes, the fundamentals of what protein language models are and how one can use them for sequence annotation, the strengths and weaknesses of these models, and future directions toward developing better models for viral annotation more broadly.
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Affiliation(s)
- Zachary N. Flamholz
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Charlotte Li
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Libusha Kelly
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
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5
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Ares-Arroyo M, Coluzzi C, Moura de Sousa JA, Rocha EPC. Hijackers, hitchhikers, or co-drivers? The mysteries of mobilizable genetic elements. PLoS Biol 2024; 22:e3002796. [PMID: 39208359 PMCID: PMC11389934 DOI: 10.1371/journal.pbio.3002796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/11/2024] [Indexed: 09/04/2024] Open
Abstract
Mobile genetic elements shape microbial gene repertoires and populations. Recent results reveal that many, possibly most, microbial mobile genetic elements require helpers to transfer between genomes, which we refer to as Hitcher Genetic Elements (hitchers or HGEs). They may be a large fraction of pathogenicity and resistance genomic islands, whose mechanisms of transfer have remained enigmatic for decades. Together with their helper elements and their bacterial hosts, hitchers form tripartite networks of interactions that evolve rapidly within a parasitism-mutualism continuum. In this emerging view of microbial genomes as communities of mobile genetic elements many questions arise. Which elements are being moved, by whom, and how? How often are hitchers costly hyper-parasites or beneficial mutualists? What is the evolutionary origin of hitchers? Are there key advantages associated with hitchers' lifestyle that justify their unexpected abundance? And why are hitchers systematically smaller than their helpers? In this essay, we start answering these questions and point ways ahead for understanding the principles, origin, mechanisms, and impact of hitchers in bacterial ecology and evolution.
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Affiliation(s)
- Manuel Ares-Arroyo
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Charles Coluzzi
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Jorge A Moura de Sousa
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
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6
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Beamud B, Benz F, Bikard D. Going viral: The role of mobile genetic elements in bacterial immunity. Cell Host Microbe 2024; 32:804-819. [PMID: 38870898 DOI: 10.1016/j.chom.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024]
Abstract
Bacteriophages and other mobile genetic elements (MGEs) pose a significant threat to bacteria, subjecting them to constant attacks. In response, bacteria have evolved a sophisticated immune system that employs diverse defensive strategies and mechanisms. Remarkably, a growing body of evidence suggests that most of these defenses are encoded by MGEs themselves. This realization challenges our traditional understanding of bacterial immunity and raises intriguing questions about the evolutionary forces at play. Our review provides a comprehensive overview of the latest findings on the main families of MGEs and the defense systems they encode. We also highlight how a vast diversity of defense systems remains to be discovered and their mechanism of mobility understood. Altogether, the composition and distribution of defense systems in bacterial genomes only makes sense in the light of the ecological and evolutionary interactions of a complex network of MGEs.
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Affiliation(s)
- Beatriz Beamud
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France.
| | - Fabienne Benz
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | - David Bikard
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France.
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7
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Angulo-Cánovas E, Bartual A, López-Igual R, Luque I, Radzinski NP, Shilova I, Anjur-Dietrich M, García-Jurado G, Úbeda B, González-Reyes JA, Díez J, Chisholm SW, García-Fernández JM, del Carmen Muñoz-Marín M. Direct interaction between marine cyanobacteria mediated by nanotubes. SCIENCE ADVANCES 2024; 10:eadj1539. [PMID: 38781331 PMCID: PMC11114229 DOI: 10.1126/sciadv.adj1539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
Microbial associations and interactions drive and regulate nutrient fluxes in the ocean. However, physical contact between cells of marine cyanobacteria has not been studied thus far. Here, we show a mechanism of direct interaction between the marine cyanobacteria Prochlorococcus and Synechococcus, the intercellular membrane nanotubes. We present evidence of inter- and intra-genus exchange of cytoplasmic material between neighboring and distant cells of cyanobacteria mediated by nanotubes. We visualized and measured these structures in xenic and axenic cultures and in natural samples. We show that nanotubes are produced between living cells, suggesting that this is a relevant system of exchange material in vivo. The discovery of nanotubes acting as exchange bridges in the most abundant photosynthetic organisms in the ocean may have important implications for their interactions with other organisms and their population dynamics.
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Affiliation(s)
- Elisa Angulo-Cánovas
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba 14014, Spain
| | - Ana Bartual
- Instituto Universitario de Investigaciones Marinas (INMAR), Campus de Excelencia Internacional del Mar (CEI·MAR), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Rocío López-Igual
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain
| | - Ignacio Luque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Sevilla, Spain
| | - Nikolai P. Radzinski
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Maya Anjur-Dietrich
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gema García-Jurado
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Bárbara Úbeda
- Instituto Universitario de Investigaciones Marinas (INMAR), Campus de Excelencia Internacional del Mar (CEI·MAR), Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - José Antonio González-Reyes
- Departamento de Biología Celular, Fisiología e Inmunología, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba 14014, Spain
| | - Jesús Díez
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba 14014, Spain
| | - Sallie W. Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - José Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba 14014, Spain
| | - María del Carmen Muñoz-Marín
- Departamento de Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba 14014, Spain
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8
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Van Duyne GD, Landy A. Bacteriophage lambda site-specific recombination. Mol Microbiol 2024; 121:895-911. [PMID: 38372210 PMCID: PMC11096046 DOI: 10.1111/mmi.15241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
The site-specific recombination pathway of bacteriophage λ encompasses isoenergetic but highly directional and tightly regulated integrative and excisive reactions that integrate and excise the vial chromosome into and out of the bacterial chromosome. The reactions require 240 bp of phage DNA and 21 bp of bacterial DNA comprising 16 protein binding sites that are differentially used in each pathway by the phage-encoded Int and Xis proteins and the host-encoded integration host factor and factor for inversion stimulation proteins. Structures of higher-order protein-DNA complexes of the four-way Holliday junction recombination intermediates provided clarifying insights into the mechanisms, directionality, and regulation of these two pathways, which are tightly linked to the physiology of the bacterial host cell. Here we review our current understanding of the mechanisms responsible for regulating and executing λ site-specific recombination, with an emphasis on key studies completed over the last decade.
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Affiliation(s)
- Gregory D Van Duyne
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Arthur Landy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
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9
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Stein AM, Biller SJ. An ocean of diffusible information. Trends Genet 2024; 40:209-210. [PMID: 38310066 DOI: 10.1016/j.tig.2024.01.007] [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: 01/15/2024] [Accepted: 01/22/2024] [Indexed: 02/05/2024]
Abstract
In the ocean, free-living bacteria exist in a dilute world where direct physical interactions between cells are relatively rare. How then do they exchange genetic information via horizontal gene transfer (HGT)? Lücking et al. have explored the world of marine 'protected extracellular DNA' (peDNA), and find that extracellular vesicles (EVs) are likely to play an important role.
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Affiliation(s)
- Ashley M Stein
- Wellesley College, Department of Biological Sciences, Wellesley, MA 02481, USA
| | - Steven J Biller
- Wellesley College, Department of Biological Sciences, Wellesley, MA 02481, USA.
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10
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Flamholz ZN, Biller SJ, Kelly L. Large language models improve annotation of prokaryotic viral proteins. Nat Microbiol 2024; 9:537-549. [PMID: 38287147 PMCID: PMC11311208 DOI: 10.1038/s41564-023-01584-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 12/08/2023] [Indexed: 01/31/2024]
Abstract
Viral genomes are poorly annotated in metagenomic samples, representing an obstacle to understanding viral diversity and function. Current annotation approaches rely on alignment-based sequence homology methods, which are limited by the paucity of characterized viral proteins and divergence among viral sequences. Here we show that protein language models can capture prokaryotic viral protein function, enabling new portions of viral sequence space to be assigned biologically meaningful labels. When applied to global ocean virome data, our classifier expanded the annotated fraction of viral protein families by 29%. Among previously unannotated sequences, we highlight the identification of an integrase defining a mobile element in marine picocyanobacteria and a capsid protein that anchors globally widespread viral elements. Furthermore, improved high-level functional annotation provides a means to characterize similarities in genomic organization among diverse viral sequences. Protein language models thus enhance remote homology detection of viral proteins, serving as a useful complement to existing approaches.
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Affiliation(s)
- Zachary N Flamholz
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Steven J Biller
- Department of Biological Sciences, Wellesley College, Wellesley, MA, USA
| | - Libusha Kelly
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.
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11
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Barcia-Cruz R, Goudenège D, Moura de Sousa JA, Piel D, Marbouty M, Rocha EPC, Le Roux F. Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages. Nat Commun 2024; 15:664. [PMID: 38253718 PMCID: PMC10803314 DOI: 10.1038/s41467-024-44965-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Phage satellites are bacterial genetic elements that co-opt phage machinery for their own dissemination. Here we identify a family of satellites, named Phage-Inducible Chromosomal Minimalist Islands (PICMIs), that are broadly distributed in marine bacteria of the family Vibrionaceae. A typical PICMI is characterized by reduced gene content, does not encode genes for capsid remodelling, and packages its DNA as a concatemer. PICMIs integrate in the bacterial host genome next to the fis regulator, and encode three core proteins necessary for excision and replication. PICMIs are dependent on virulent phage particles to spread to other bacteria, and protect their hosts from other competitive phages without interfering with their helper phage. Thus, our work broadens our understanding of phage satellites and narrows down the minimal number of functions necessary to hijack a tailed phage.
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Affiliation(s)
- Rubén Barcia-Cruz
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - David Goudenège
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, CS 10070, F-29280, Plouzané, France
| | - Jorge A Moura de Sousa
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Damien Piel
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, CS 10070, F-29280, Plouzané, France
| | - Martial Marbouty
- Institut Pasteur, Université Paris Cité, Organization and Dynamics of Viral Genomes Group, CNRS UMR 3525, Paris, F-75015, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Frédérique Le Roux
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France.
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, CS 10070, F-29280, Plouzané, France.
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Canada.
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12
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Ahmed AAQ, McKay TJM. Environmental and ecological importance of bacterial extracellular vesicles (BEVs). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:168098. [PMID: 37884154 DOI: 10.1016/j.scitotenv.2023.168098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/24/2023] [Accepted: 10/22/2023] [Indexed: 10/28/2023]
Abstract
Extracellular vesicles are unique structures released by the cells of all life forms. Bacterial extracellular vesicles (BEVs) were found in various ecosystems and natural habitats. They are associated with bacterial-bacterial interactions as well as host-bacterial interactions in the environment. Moreover, BEVs facilitate bacterial adaptation to a variety of environmental conditions. BEVs were found to be abundant in the environment, and therefore they can regulate a broad range of environmental processes. In the environment, BEVs can serve as tools for cell-to-cell interaction, secreting mechanism of unwanted materials, transportation, genetic materials exchange and storage, defense and protection, growth support, electron transfer, and cell-surface interplay regulation. Thus, BEVs have a great potential to be used in a variety of environmental applications such as serving as bioremediating reagents for environmental disaster mitigation as well as removing problematic biofilms and waste treatment. This research area needs to be investigated further to disclose the full environmental and ecological importance of BEVs as well as to investigate how to harness BEVs as effective tools in a variety of environmental applications.
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Affiliation(s)
- Abeer Ahmed Qaed Ahmed
- Department of Environmental Sciences, School of Ecological and Human Sustainability, College of Agriculture and Environmental Sciences, University of South Africa, P.O. Box 392, Florida, Johannesburg 1710, South Africa.
| | - Tracey Jill Morton McKay
- Department of Environmental Sciences, School of Ecological and Human Sustainability, College of Agriculture and Environmental Sciences, University of South Africa, P.O. Box 392, Florida, Johannesburg 1710, South Africa
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13
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Wang S, He B, Wu H, Cai Q, Ramírez-Sánchez O, Abreu-Goodger C, Birch PRJ, Jin H. Plant mRNAs move into a fungal pathogen via extracellular vesicles to reduce infection. Cell Host Microbe 2024; 32:93-105.e6. [PMID: 38103543 PMCID: PMC10872371 DOI: 10.1016/j.chom.2023.11.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/17/2023] [Accepted: 11/20/2023] [Indexed: 12/19/2023]
Abstract
Cross-kingdom small RNA trafficking between hosts and microbes modulates gene expression in the interacting partners during infection. However, whether other RNAs are also transferred is unclear. Here, we discover that host plant Arabidopsis thaliana delivers mRNAs via extracellular vesicles (EVs) into the fungal pathogen Botrytis cinerea. A fluorescent RNA aptamer reporter Broccoli system reveals host mRNAs in EVs and recipient fungal cells. Using translating ribosome affinity purification profiling and polysome analysis, we observe that delivered host mRNAs are translated in fungal cells. Ectopic expression of two transferred host mRNAs in B. cinerea shows that their proteins are detrimental to infection. Arabidopsis knockout mutants of the genes corresponding to these transferred mRNAs are more susceptible. Thus, plants have a strategy to reduce infection by transporting mRNAs into fungal cells. mRNAs transferred from plants to pathogenic fungi are translated to compromise infection, providing knowledge that helps combat crop diseases.
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Affiliation(s)
- Shumei Wang
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Baoye He
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Huaitong Wu
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Qiang Cai
- State Key Laboratory of Hybrid Rice, College of Life Science, Wuhan University, Wuhan, China
| | - Obed Ramírez-Sánchez
- National Laboratory of Genomics for Biodiversity (Langebio), Cinvestav, Irapuato 36821 Guanajuato, Mexico
| | - Cei Abreu-Goodger
- Institute of Ecology and Evolution, School of Biological Sciences, the University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Paul R J Birch
- Division of Plant Sciences, School of Life Science, University of Dundee at James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA.
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14
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Layoun P, López-Pérez M, Haro-Moreno JM, Haber M, Thrash JC, Henson MW, Kavagutti VS, Ghai R, Salcher MM. Flexible genomic island conservation across freshwater and marine Methylophilaceae. THE ISME JOURNAL 2024; 18:wrad036. [PMID: 38365254 PMCID: PMC10872708 DOI: 10.1093/ismejo/wrad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 02/18/2024]
Abstract
The evolutionary trajectory of Methylophilaceae includes habitat transitions from freshwater sediments to freshwater and marine pelagial that resulted in genome reduction (genome-streamlining) of the pelagic taxa. However, the extent of genetic similarities in the genomic structure and microdiversity of the two genome-streamlined pelagic lineages (freshwater "Ca. Methylopumilus" and the marine OM43 lineage) has so far never been compared. Here, we analyzed complete genomes of 91 "Ca. Methylopumilus" strains isolated from 14 lakes in Central Europe and 12 coastal marine OM43 strains. The two lineages showed a remarkable niche differentiation with clear species-specific differences in habitat preference and seasonal distribution. On the other hand, we observed a synteny preservation in their genomes by having similar locations and types of flexible genomic islands (fGIs). Three main fGIs were identified: a replacement fGI acting as phage defense, an additive fGI harboring metabolic and resistance-related functions, and a tycheposon containing nitrogen-, thiamine-, and heme-related functions. The fGIs differed in relative abundances in metagenomic datasets suggesting different levels of variability ranging from strain-specific to population-level adaptations. Moreover, variations in one gene seemed to be responsible for different growth at low substrate concentrations and a potential biogeographic separation within one species. Our study provides a first insight into genomic microdiversity of closely related taxa within the family Methylophilaceae and revealed remarkably similar dynamics involving mobile genetic elements and recombination between freshwater and marine family members.
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Affiliation(s)
- Paul Layoun
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 San Juan de Alicante, Spain
| | - Jose M Haro-Moreno
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, 03550 San Juan de Alicante, Spain
| | - Markus Haber
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Michael W Henson
- Department of Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Vinicius Silva Kavagutti
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
| | - Michaela M Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, 37005 Ceske Budejovice, Czech Republic
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15
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Tokuda M, Shintani M. Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol 2024; 17:e14408. [PMID: 38226780 PMCID: PMC10832538 DOI: 10.1111/1751-7915.14408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Mobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini-review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.
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Affiliation(s)
- Maho Tokuda
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
| | - Masaki Shintani
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
- Research Institute of Green Science and TechnologyShizuoka UniversityHamamatsuJapan
- Japan Collection of MicroorganismsRIKEN BioResource Research CenterIbarakiJapan
- Graduate School of Integrated Science and TechnologyShizuoka UniversityHamamatsuJapan
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16
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Tao Y, He C, Lin D, Gu Z, Pu W. Comprehensive Identification of Mitochondrial Pseudogenes (NUMTs) in the Human Telomere-to-Telomere Reference Genome. Genes (Basel) 2023; 14:2092. [PMID: 38003036 PMCID: PMC10671835 DOI: 10.3390/genes14112092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Practices related to mitochondrial research have long been hindered by the presence of mitochondrial pseudogenes within the nuclear genome (NUMTs). Even though partially assembled human reference genomes like hg38 have included NUMTs compilation, the exhaustive NUMTs within the only complete reference genome (T2T-CHR13) remain unknown. Here, we comprehensively identified the fixed NUMTs within the reference genome using human pan-mitogenome (HPMT) from GeneBank. The inclusion of HPMT serves the purpose of establishing an authentic mitochondrial DNA (mtDNA) mutational spectrum for the identification of NUMTs, distinguishing it from the polymorphic variations found in NUMTs. Using HPMT, we identified approximately 10% of additional NUMTs in three human reference genomes under stricter thresholds. And we also observed an approximate 6% increase in NUMTs in T2T-CHR13 compared to hg38, including NUMTs on the short arms of chromosomes 13, 14, and 15 that were not assembled previously. Furthermore, alignments based on 20-mer from mtDNA suggested the presence of more mtDNA-like short segments within the nuclear genome, which should be avoided for short amplicon or cell free mtDNA detection. Finally, through the assay of transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) on cell lines before and after mtDNA elimination, we concluded that NUMTs have a minimal impact on bulk ATAC-seq, even though 16% of sequencing data originated from mtDNA.
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Affiliation(s)
- Yichen Tao
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China; (Y.T.); (D.L.)
| | - Chengpeng He
- Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Nansha District, Guangzhou 511458, China;
| | - Deng Lin
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China; (Y.T.); (D.L.)
| | - Zhenglong Gu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China; (Y.T.); (D.L.)
- Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Nansha District, Guangzhou 511458, China;
| | - Weilin Pu
- Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Nansha District, Guangzhou 511458, China;
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17
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Lücking D, Mercier C, Alarcón-Schumacher T, Erdmann S. Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space. ISME COMMUNICATIONS 2023; 3:112. [PMID: 37848554 PMCID: PMC10582014 DOI: 10.1038/s43705-023-00317-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/28/2023] [Accepted: 10/05/2023] [Indexed: 10/19/2023]
Abstract
Environmental virus metagenomes, commonly referred to as "viromes", are typically generated by physically separating virus-like particles (VLPs) from the microbial fraction based on their size and mass. However, most methods used to purify VLPs, enrich extracellular vesicles (EVs) and gene transfer agents (GTAs) simultaneously. Consequently, the sequence space traditionally referred to as a "virome" contains host-associated sequences, transported via EVs or GTAs. We therefore propose to call the genetic material isolated from size-fractionated (0.22 µm) and DNase-treated samples protected environmental DNA (peDNA). This sequence space contains viral genomes, DNA transduced by viruses and DNA transported in EVs and GTAs. Since there is no genetic signature for peDNA transported in EVs, GTAs and virus particles, we rely on the successful removal of contaminating remaining cellular and free DNA when analyzing peDNA. Using marine samples collected from the North Sea, we generated a thoroughly purified peDNA dataset and developed a bioinformatic pipeline to determine the potential origin of the purified DNA. This pipeline was applied to our dataset as well as existing global marine "viromes". Through this pipeline, we identified known GTA and EV producers, as well as organisms with actively transducing proviruses as the source of the peDNA, thus confirming the reliability of our approach. Additionally, we identified novel and widespread EV producers, and found quantitative evidence suggesting that EV-mediated gene transfer plays a significant role in driving horizontal gene transfer (HGT) in the world's oceans.
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Affiliation(s)
- Dominik Lücking
- Max-Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Coraline Mercier
- Max-Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | | | - Susanne Erdmann
- Max-Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
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18
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Ustick LJ, Larkin AA, Martiny AC. Global scale phylogeography of functional traits and microdiversity in Prochlorococcus. THE ISME JOURNAL 2023; 17:1671-1679. [PMID: 37454234 PMCID: PMC10504305 DOI: 10.1038/s41396-023-01469-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenome-assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenome-assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype's phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus.
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Affiliation(s)
- Lucas J Ustick
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
- Structural and Computational Biology Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alyse A Larkin
- Department of Earth System Science, University of California Irvine, Irvine, CA, 92697, USA
- Global Ocean Monitoring and Observing, National Oceanic and Atmospheric Administration, Washington, DC, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA.
- Department of Earth System Science, University of California Irvine, Irvine, CA, 92697, USA.
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19
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Bucknell AH, McDonald MC. That's no moon, it's a Starship: Giant transposons driving fungal horizontal gene transfer. Mol Microbiol 2023; 120:555-563. [PMID: 37434470 DOI: 10.1111/mmi.15118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 07/13/2023]
Abstract
To date, most reports of horizontal gene transfer (HGT) in fungi rely on genome sequence data and are therefore an indirect measure of HGT after the event has occurred. However, a novel group of class II-like transposons known as Starships may soon alter this status quo. Starships are giant transposable elements that carry dozens of genes, some of which are host-beneficial, and are linked to many recent HGT events in the fungal kingdom. These transposons remain active and mobile in many fungal genomes and their transposition has recently been shown to be driven by a conserved tyrosine-recombinase called 'Captain'. This perspective explores some of the remaining unanswered questions about how these Starship transposons move, both within a genome and between different species. We seek to outline several experimental approaches that can be used to identify the genes essential for Starship-mediated HGT and draw links to other recently discovered giant transposons outside of the fungal kingdom.
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Affiliation(s)
- Angus H Bucknell
- School of Biosciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Megan C McDonald
- School of Biosciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
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20
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Johnson MC, Laderman E, Huiting E, Zhang C, Davidson A, Bondy-Denomy J. Core defense hotspots within Pseudomonas aeruginosa are a consistent and rich source of anti-phage defense systems. Nucleic Acids Res 2023; 51:4995-5005. [PMID: 37140042 PMCID: PMC10250203 DOI: 10.1093/nar/gkad317] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 05/05/2023] Open
Abstract
Bacteria use a diverse arsenal of anti-phage immune systems, including CRISPR-Cas and restriction enzymes. Recent advances in anti-phage system discovery and annotation tools have unearthed many unique systems, often encoded in horizontally transferred defense islands, which can be horizontally transferred. Here, we developed Hidden Markov Models (HMMs) for defense systems and queried microbial genomes on the NCBI database. Out of the 30 species with >200 completely sequenced genomes, our analysis found Pseudomonas aeruginosa exhibits the greatest diversity of anti-phage systems, as measured by Shannon entropy. Using network analysis to identify the common neighbors of anti-phage systems, we identified two core defense hotspot loci (cDHS1 and cDHS2). cDHS1 is up to 224 kb (median: 26 kb) with varied arrangements of more than 30 distinct immune systems across isolates, while cDHS2 has 24 distinct systems (median: 6 kb). Both cDHS regions are occupied in a majority of P. aeruginosa isolates. Most cDHS genes are of unknown function potentially representing new anti-phage systems, which we validated by identifying a novel anti-phage system (Shango) commonly encoded in cDHS1. Identifying core genes flanking immune islands could simplify immune system discovery and may represent popular landing spots for diverse MGEs carrying anti-phage systems.
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Affiliation(s)
- Matthew C Johnson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Eric Laderman
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Erin Huiting
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Chi Zhang
- Departments of Biochemistry and Molecular Genetics, University of Toronto, 661 University Ave, Toronto, ON M5G 1M1, Canada
| | - Alan Davidson
- Departments of Biochemistry and Molecular Genetics, University of Toronto, 661 University Ave, Toronto, ON M5G 1M1, Canada
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Innovative Genomics Institute, Berkeley, CA 94720, USA
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21
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Birzu G, Muralidharan HS, Goudeau D, Malmstrom RR, Fisher DS, Bhaya D. Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543983. [PMID: 37333348 PMCID: PMC10274767 DOI: 10.1101/2023.06.06.543983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Bacterial species often undergo rampant recombination yet maintain cohesive genomic identity. Ecological differences can generate recombination barriers between species and sustain genomic clusters in the short term. But can these forces prevent genomic mixing during long-term coevolution? Cyanobacteria in Yellowstone hot springs comprise several diverse species that have coevolved for hundreds of thousands of years, providing a rare natural experiment. By analyzing more than 300 single-cell genomes, we show that despite each species forming a distinct genomic cluster, much of the diversity within species is the result of hybridization driven by selection, which has mixed their ancestral genotypes. This widespread mixing is contrary to the prevailing view that ecological barriers can maintain cohesive bacterial species and highlights the importance of hybridization as a source of genomic diversity.
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Affiliation(s)
- Gabriel Birzu
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | | | - Danielle Goudeau
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rex R. Malmstrom
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Daniel S. Fisher
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Devaki Bhaya
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
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22
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de Sousa JM, Fillol-Salom A, Penadés JR, Rocha EC. Identification and characterization of thousands of bacteriophage satellites across bacteria. Nucleic Acids Res 2023; 51:2759-2777. [PMID: 36869669 PMCID: PMC10085698 DOI: 10.1093/nar/gkad123] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/19/2023] [Accepted: 02/10/2023] [Indexed: 03/05/2023] Open
Abstract
Bacteriophage-bacteria interactions are affected by phage satellites, elements that exploit phages for transfer between bacteria. Satellites can encode defense systems, antibiotic resistance genes, and virulence factors, but their number and diversity are unknown. We developed SatelliteFinder to identify satellites in bacterial genomes, detecting the four best described families: P4-like, phage inducible chromosomal islands (PICI), capsid-forming PICI, and PICI-like elements (PLE). We vastly expanded the number of described elements to ∼5000, finding bacterial genomes with up to three different families of satellites. Most satellites were found in Proteobacteria and Firmicutes, but some are in novel taxa such as Actinobacteria. We characterized the gene repertoires of satellites, which are variable in size and composition, and their genomic organization, which is very conserved. Phylogenies of core genes in PICI and cfPICI indicate independent evolution of their hijacking modules. There are few other homologous core genes between other families of satellites, and even fewer homologous to phages. Hence, phage satellites are ancient, diverse, and probably evolved multiple times independently. Given the many bacteria infected by phages that still lack known satellites, and the recent proposals for novel families, we speculate that we are at the beginning of the discovery of massive numbers and types of satellites.
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Affiliation(s)
- Jorge A Moura de Sousa
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
| | - Alfred Fillol-Salom
- Center for Bacterial Resistance Biology, Imperial College London, London, SW7 2AZ, UK
| | - José R Penadés
- Center for Bacterial Resistance Biology, Imperial College London, London, SW7 2AZ, UK
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris 75015, France
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23
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Dart E, Ahlgren NA. New tRNA-targeting transposons that hijack phage and vesicles. Trends Genet 2023; 39:433-435. [PMID: 37019751 DOI: 10.1016/j.tig.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/15/2023] [Indexed: 04/07/2023]
Abstract
Genomic islands are hotspots for horizontal gene transfer (HGT) in bacteria, but, for Prochlorococcus, an abundant marine cyanobacterium, how these islands form has puzzled scientists. With the discovery of tycheposons, a new family of transposons, Hackl et al. provide evidence for elegant new mechanisms of gene rearrangement and transfer among Prochlorococcus and bacteria more broadly.
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Affiliation(s)
- Emily Dart
- Department of Biology, Clark University, Worcester, MA 01610, USA
| | - Nathan A Ahlgren
- Department of Biology, Clark University, Worcester, MA 01610, USA.
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24
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Berta-Thompson JW, Thomas E, Cubillos-Ruiz A, Hackl T, Becker JW, Coe A, Biller SJ, Berube PM, Chisholm SW. Draft genomes of three closely related low light-adapted Prochlorococcus. BMC Genom Data 2023; 24:11. [PMID: 36829130 PMCID: PMC9951446 DOI: 10.1186/s12863-022-01103-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 12/21/2022] [Indexed: 02/26/2023] Open
Abstract
OBJECTIVES The marine cyanobacterium Prochlorococcus is a critical part of warm ocean ecosystems and a model for studying microbial evolution and ecology. To expand the representation of this organism's vast wild diversity in sequence collections, we performed a set of isolation efforts targeting low light-adapted Prochlorococcus. Three genomes resulting from this larger body of work are described here. DATA DESCRIPTION We present draft-quality Prochlorococcus genomes from enrichment cultures P1344, P1361, and P1363, sampled in the North Pacific. The genomes were built from Illumina paired reads assembled de novo. Supporting datasets of raw reads, assessments, and sequences from co-enriched heterotrophic marine bacteria are also provided. These three genomes represent members of the low light-adapted LLIV Prochlorococcus clade that are closely related, with 99.9% average nucleotide identity between pairs, yet vary in gene content. Expanding the powerful toolkit of Prochlorococcus genomes, these sequences provide an opportunity to study fine-scale variation and microevolutionary processes.
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Affiliation(s)
- Jessie W Berta-Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Research and Conservation, Denver Botanic Gardens, Denver, CO, 80206, USA.
| | - Elaina Thomas
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Andrés Cubillos-Ruiz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Thomas Hackl
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, 9700 CC, The Netherlands
| | - Jamie W Becker
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Science and Mathematics, Alvernia University, Reading, PA, 19607, USA
| | - Allison Coe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Steven J Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Biological Sciences, Wellesley College, Wellesley, MA, 02481, USA
| | - Paul M Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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25
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Utter DR, Orphan VJ. Gifts hidden in shadowy genome islands. Cell 2023; 186:5-7. [PMID: 36608658 DOI: 10.1016/j.cell.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 01/07/2023]
Abstract
Despite being typically perceived as "clonal" organisms, bacteria and archaea possess numerous mechanisms to share and co-opt genetic material from other lineages. Several mechanisms for horizontal gene transfer have been discovered, but the high mosaicity observed in many bacterial genomes outscales that explained by known mechanisms, hinting at yet undiscovered processes. In this issue of Cell, Hackl et al. introduce a new category of mobile genetic elements called tycheposons, providing a novel mechanism that contributes to the prodigious genomic diversity within microbial populations. The discovery and characterization of tycheposons prompts a reevaluation of microbial diversification in complex environments.
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Affiliation(s)
- D R Utter
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - V J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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