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Kolan D, Cattan-Tsaushu E, Enav H, Freiman Z, Malinsky-Rushansky N, Ninio S, Avrani S. Tradeoffs between phage resistance and nitrogen fixation drive the evolution of genes essential for cyanobacterial heterocyst functionality. ISME J 2024; 18:wrad008. [PMID: 38365231 PMCID: PMC10811720 DOI: 10.1093/ismejo/wrad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 10/26/2023] [Accepted: 11/13/2023] [Indexed: 02/18/2024]
Abstract
Harmful blooms caused by diazotrophic (nitrogen-fixing) Cyanobacteria are becoming increasingly frequent and negatively impact aquatic environments worldwide. Cyanophages (viruses infecting Cyanobacteria) can potentially regulate cyanobacterial blooms, yet Cyanobacteria can rapidly acquire mutations that provide protection against phage infection. Here, we provide novel insights into cyanophage:Cyanobacteria interactions by characterizing the resistance to phages in two species of diazotrophic Cyanobacteria: Nostoc sp. and Cylindrospermopsis raciborskii. Our results demonstrate that phage resistance is associated with a fitness tradeoff by which resistant Cyanobacteria have reduced ability to fix nitrogen and/or to survive nitrogen starvation. Furthermore, we use whole-genome sequence analysis of 58 Nostoc-resistant strains to identify several mutations associated with phage resistance, including in cell surface-related genes and regulatory genes involved in the development and function of heterocysts (cells specialized in nitrogen fixation). Finally, we employ phylogenetic analyses to show that most of these resistance genes are accessory genes whose evolution is impacted by lateral gene transfer events. Together, these results further our understanding of the interplay between diazotrophic Cyanobacteria and their phages and suggest that a tradeoff between phage resistance and nitrogen fixation affects the evolution of cell surface-related genes and of genes involved in heterocyst differentiation and nitrogen fixation.
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Affiliation(s)
- Dikla Kolan
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3103301, Israel
| | - Esther Cattan-Tsaushu
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3103301, Israel
| | - Hagay Enav
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3103301, Israel
| | - Zohar Freiman
- Kinneret Limnological Laboratory (KLL) Israel Oceanographic and Limnological Research (IOLR), Migdal 1495000, Israel
| | - Nechama Malinsky-Rushansky
- Kinneret Limnological Laboratory (KLL) Israel Oceanographic and Limnological Research (IOLR), Migdal 1495000, Israel
| | - Shira Ninio
- Kinneret Limnological Laboratory (KLL) Israel Oceanographic and Limnological Research (IOLR), Migdal 1495000, Israel
| | - Sarit Avrani
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3103301, Israel
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Suzuki TA, Fitzstevens JL, Schmidt VT, Enav H, Huus KE, Ngwese MM, Grießhammer A, Pfleiderer A, Adegbite BR, Zinsou JF, Esen M, Velavan TP, Adegnika AA, Song LH, Spector TD, Muehlbauer AL, Marchi N, Kang H, Maier L, Blekhman R, Ségurel L, Ko G, Youngblut ND, Kremsner P, Ley RE. Codiversification of gut microbiota with humans. Science 2022; 377:1328-1332. [PMID: 36108023 PMCID: PMC10777373 DOI: 10.1126/science.abm7759] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia, and Africa, including mothers and their children. Between and within countries, a parallel evolutionary history was evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes.
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Affiliation(s)
- Taichi A. Suzuki
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - J. Liam Fitzstevens
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Victor T. Schmidt
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Hagay Enav
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Kelsey E. Huus
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Mirabeau Mbong Ngwese
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Anne Grießhammer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Anne Pfleiderer
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Bayode R. Adegbite
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Jeannot F. Zinsou
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Meral Esen
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Thirumalaisamy P. Velavan
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Vietnamese German Center for Medical Research, Hanoi, Vietnam
| | - Ayola A. Adegnika
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- German Center for Infection Research, Tübingen, Germany
- Fondation pour la Recherche Scientifique, Cotonou, Bénin
| | - Le Huu Song
- Vietnamese German Center for Medical Research, Hanoi, Vietnam
- 108 Military Central Hospital, Hanoi, Vietnam
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Amanda L. Muehlbauer
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA
| | - Nina Marchi
- Eco-anthropologie, Muséum National d’Histoire Naturelle, CNRS, Université de Paris, Paris, France
| | - Hyena Kang
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Lisa Maier
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Laure Ségurel
- Eco-anthropologie, Muséum National d’Histoire Naturelle, CNRS, Université de Paris, Paris, France
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, Université Lyon 1, Villeurbanne, France
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Nicholas D. Youngblut
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Peter Kremsner
- Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- German Center for Infection Research, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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Abstract
At birth, neonates provide a vast habitat awaiting microbial colonization. Microbiome assembly is a complex process involving microbial seeding and succession driven by ecological forces and subject to environmental conditions. These successional events not only significantly affect the ecology and function of the microbiome, but also impact host health. While the establishment of the infant microbiome has been a point of interest for decades, an integrated view focusing on strain level colonization has been lacking until recently. Technological and computational advancements enabling strain-level analyses of the infant microbiome have demonstrated the immense complexity of this system and allowed for an improved understanding of how strains of the same species spread, colonize, evolve, and affect the host. Here, we review the current knowledge of the establishment and maturation of the infant gut microbiome with particular emphasis on newer discoveries achieved through strain-centric analyses.
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Affiliation(s)
- Hagay Enav
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany; Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.
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Laloum E, Cattan-Tsaushu E, Schwartz DA, Shaalan H, Enav H, Kolan D, Avrani S. Isolation and characterization of a novel Lambda-like phage infecting the bloom-forming cyanobacteria Cylindrospermopsis raciborskii. Environ Microbiol 2022; 24:2435-2448. [PMID: 35049139 PMCID: PMC9303873 DOI: 10.1111/1462-2920.15908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/14/2022] [Indexed: 11/28/2022]
Abstract
Cylindrospermopsis raciborskii is a central bloom‐forming cyanobacteria. However, despite its ecological significance, little is known of its interactions with the phages that infect it. Currently, only a single sequenced genome of a Cylindrospermopsis‐infecting phage is publicly available. Here we describe the isolation and characterization of Cr‐LKS3, a second phage infecting Cylindrospermopsis. Cr‐LKS3 is a siphovirus with a higher genome similarity to prophages within heterotrophic bacteria genomes than to any other cyanophage/cyano‐prophage, suggesting that it represents a novel cyanophage group. The function, order and orientation of the 72 genes in the Cr‐LKS3 genome are highly similar to those of Escherichia virus Lambda (hereafter Lambda), despite the very low sequence similarity between these phages, showing high evolutionary convergence despite the substantial difference in host characteristics. Similarly to Lambda, the genome of Cr‐LKS3 contains various genes that are known to be central to lysogeny, suggesting it can enter a lysogenic cycle. Cr‐LKS3 has a unique ability to infect a host with a dramatically different GC content, without carrying any tRNA genes to compensate for this difference. This ability, together with its potential lysogenic lifestyle shed light on the complex interactions between C. raciborskii and its phages.
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Affiliation(s)
- Emmanuelle Laloum
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa, Israel
| | - Esther Cattan-Tsaushu
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa, Israel
| | | | - Hanaa Shaalan
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa, Israel
| | - Hagay Enav
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dikla Kolan
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa, Israel
| | - Sarit Avrani
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa, Israel
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Enav H, Kirzner S, Lindell D, Mandel-Gutfreund Y, Béjà O. Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean. Nat Commun 2018; 9:4698. [PMID: 30409965 PMCID: PMC6224464 DOI: 10.1038/s41467-018-07164-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/22/2018] [Indexed: 12/16/2022] Open
Abstract
Cyanophages of the Myoviridae family include generalist viruses capable of infecting a wide range of hosts including those from different cyanobacterial genera. While the influence of phages on host evolution has been studied previously, it is not known how the infection of distinct hosts influences the evolution of cyanophage populations. Here, using an experimental evolution approach, we investigated the adaptation of multiple cyanophage populations to distinct cyanobacterial hosts. We show that when infecting an "optimal" host, whose infection is the most efficient, phage populations accumulated only a few mutations. However, when infecting "sub-optimal" hosts, different mutations spread in the phage populations, leading to rapid diversification into distinct subpopulations. Based on our results, we propose a model demonstrating how shifts in microbial abundance, which lead to infection of "sub-optimal" hosts, act as a driver for rapid diversification of viral populations.
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Affiliation(s)
- Hagay Enav
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel. .,Department of Microbiome Science, Max-Planck Institute for Developmental Biology, 72076, Tübingen, Germany.
| | - Shay Kirzner
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Debbie Lindell
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel.,Department of Computer Sciences, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel.
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Hevroni G, Enav H, Rohwer F, Béjà O. Diversity of viral photosystem-I psaA genes. ISME J 2014; 9:1892-8. [PMID: 25535938 PMCID: PMC4511924 DOI: 10.1038/ismej.2014.244] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/11/2014] [Accepted: 11/17/2014] [Indexed: 12/23/2022]
Abstract
Marine photosynthesis is one of the major contributors to the global carbon cycle and the world's oxygen supply. This process is largely driven by cyanobacteria, namely Synechococcus and Prochlorococcus. Genes encoding photosystem-II (PSII) reaction center proteins are found in many cyanophage genomes, and are expressed during the infection of their hosts. On the basis of metagenomics, cyanophage photosystem-I (PSI) gene cassettes were recently discovered with two gene arrangements psaJF→C→A→B→K→E→D and psaD→C→A→B. It was suggested that the horizontal transfer of PSII and PSI genes is increasing phage fitness. To better understand their diversity, we designed degenerate primers to cover a wide diversity of organisms, and using PCR we targeted the psaC→A arrangement, which is unique to cyanophages cassettes. We examined viral concentrates from four islands in the Pacific Ocean and found samples containing the psaC→A arrangement. Analyses of the amplified viral psaA gene revealed six subgroups varying in their level of similarity and %G+C content, suggesting that the diversity of cyanophage PSI genes is greater than originally thought.
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Affiliation(s)
- Gur Hevroni
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hagay Enav
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Oded Béjà
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
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Enav H, Mandel-Gutfreund Y, Béjà O. Comparative metagenomic analyses reveal viral-induced shifts of host metabolism towards nucleotide biosynthesis. Microbiome 2014; 2:9. [PMID: 24666644 PMCID: PMC4022391 DOI: 10.1186/2049-2618-2-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 02/13/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Viral genomes often contain metabolic genes that were acquired from host genomes (auxiliary genes). It is assumed that these genes are fixed in viral genomes as a result of a selective force, favoring viruses that acquire specific metabolic functions. While many individual auxiliary genes were observed in viral genomes and metagenomes, there is great importance in investigating the abundance of auxiliary genes and metabolic functions in the marine environment towards a better understanding of their role in promoting viral reproduction. RESULTS In this study, we searched for enriched viral auxiliary genes and mapped them to metabolic pathways. To initially identify enriched auxiliary genes, we analyzed metagenomic microbial reads from the Global Ocean Survey (GOS) dataset that were characterized as viral, as well as marine virome and microbiome datasets from the Line Islands. Viral-enriched genes were mapped to a "global metabolism network" that comprises all KEGG metabolic pathways. Our analysis of the viral-enriched pathways revealed that purine and pyrimidine metabolism pathways are among the most enriched pathways. Moreover, many other viral-enriched metabolic pathways were found to be closely associated with the purine and pyrimidine metabolism pathways. Furthermore, we observed that sequential reactions are promoted in pathways having a high proportion of enriched genes. In addition, these enriched genes were found to be of modular nature, participating in several pathways. CONCLUSIONS Our naïve metagenomic analyses strongly support the well-established notion that viral auxiliary genes promote viral replication via both degradation of host DNA and RNA as well as a shift of the host metabolism towards nucleotide biosynthesis, clearly indicating that comparative metagenomics can be used to understand different environments and systems without prior knowledge of pathways involved.
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Affiliation(s)
- Hagay Enav
- Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
| | | | - Oded Béjà
- Faculty of Biology, Technion Israel Institute of Technology, Haifa 32000, Israel
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El-On J, Ozer L, Gopas J, Sneir R, Enav H, Luft N, Davidov G, Golan-Goldhirsh A. Antileishmanial activity in Israeli plants. Annals of Tropical Medicine & Parasitology 2013; 103:297-306. [DOI: 10.1179/136485909x440827] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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