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Marín-Paredes R, Bolívar-Torres HH, Coronel-Gaytán A, Martínez-Romero E, Servín-Garcidueñas LE. A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseudomonadota. Curr Issues Mol Biol 2023; 45:5849-5864. [PMID: 37504286 PMCID: PMC10378326 DOI: 10.3390/cimb45070370] [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: 05/17/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023] Open
Abstract
Los Azufres National Park is a geothermal field that has a wide number of thermal manifestations; nevertheless, the microbial communities in many of these environments remain unknown. In this study, a metagenome from a sediment sample from Los Azufres National Park was sequenced. In this metagenome, we found that the microbial diversity corresponds to bacteria (Actinomycetota, Pseudomonadota), archaea (Thermoplasmatales and Candidatus Micrarchaeota and Candidatus Parvarchaeota), eukarya (Cyanidiaceae), and viruses (Fussellovirus and Caudoviricetes). The functional annotation showed genes related to the carbon fixation pathway, sulfur metabolism, genes involved in heat and cold shock, and heavy-metal resistance. From the sediment, it was possible to recover two metagenome-assembled genomes from Ferrimicrobium and Cuniculiplasma. Our results showed that there are a large number of microorganisms in Los Azufres that deserve to be studied.
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Affiliation(s)
- Roberto Marín-Paredes
- Laboratorio de Microbiómica, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58341, Mexico
| | - Hermes H Bolívar-Torres
- Escuela de Ciencias Biológicas, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia
| | - Alberto Coronel-Gaytán
- Laboratorio de Microbiómica, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58341, Mexico
| | | | - Luis E Servín-Garcidueñas
- Laboratorio de Microbiómica, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia 58341, Mexico
- Laboratorio Nacional de Análisis y Síntesis Ecológica, Escuela Nacional de Estudios Superiores Unidad Morelia, Morelia 58341, Mexico
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The Microbial Composition in Circumneutral Thermal Springs from Chignahuapan, Puebla, Mexico Reveals the Presence of Particular Sulfur-Oxidizing Bacterial and Viral Communities. Microorganisms 2020; 8:microorganisms8111677. [PMID: 33137872 PMCID: PMC7692377 DOI: 10.3390/microorganisms8111677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 12/28/2022] Open
Abstract
Terrestrial thermal springs are widely distributed globally, and these springs harbor a broad diversity of organisms of biotechnological interest. In Mexico, few studies exploring this kind of environment have been described. In this work, we explore the microbial community in Chignahuapan hot springs, which provides clues to understand these ecosystems' diversity. We assessed the diversity of the microorganism communities in a hot spring environment with a metagenomic shotgun approach. Besides identifying similarities and differences with other ecosystems, we achieved a systematic comparison against 11 metagenomic samples from diverse localities. The Chignahuapan hot springs show a particular prevalence of sulfur-oxidizing bacteria from the genera Rhodococcus, Thermomonas, Thiomonas, Acinetobacter, Sulfurovum, and Bacillus, highlighting those that are different from other recovered bacterial populations in circumneutral hot springs environments around the world. The co-occurrence analysis of the bacteria and viruses in these environments revealed that within the Rhodococcus, Thiomonas, Thermonas, and Bacillus genera, the Chignahuapan samples have specific species of bacteria with a particular abundance, such as Rhodococcus erytropholis. The viruses in the circumneutral hot springs present bacteriophages within the order Caudovirales (Siphoviridae, Myoviridae, and Podoviridae), but the family of Herelleviridae was the most abundant in Chignahuapan samples. Furthermore, viral auxiliary metabolic genes were identified, many of which contribute mainly to the metabolism of cofactors and vitamins as well as carbohydrate metabolism. Nevertheless, the viruses and bacteria present in the circumneutral environments contribute to the sulfur cycle. This work represents an exhaustive characterization of a community structure in samples collected from hot springs in Mexico and opens opportunities to identify organisms of biotechnological interest.
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Benavides A, Isaza JP, Niño-García JP, Alzate JF, Cabarcas F. CLAME: a new alignment-based binning algorithm allows the genomic description of a novel Xanthomonadaceae from the Colombian Andes. BMC Genomics 2018; 19:858. [PMID: 30537931 PMCID: PMC6288851 DOI: 10.1186/s12864-018-5191-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Hot spring bacteria have unique biological adaptations to survive the extreme conditions of these environments; these bacteria produce thermostable enzymes that can be used in biotechnological and industrial applications. However, sequencing these bacteria is complex, since it is not possible to culture them. As an alternative, genome shotgun sequencing of whole microbial communities can be used. The problem is that the classification of sequences within a metagenomic dataset is very challenging particularly when they include unknown microorganisms since they lack genomic reference. We failed to recover a bacterium genome from a hot spring metagenome using the available software tools, so we develop a new tool that allowed us to recover most of this genome. Results We present a proteobacteria draft genome reconstructed from a Colombian’s Andes hot spring metagenome. The genome seems to be from a new lineage within the family Rhodanobacteraceae of the class Gammaproteobacteria, closely related to the genus Dokdonella. We were able to generate this genome thanks to CLAME. CLAME, from Spanish “CLAsificador MEtagenomico”, is a tool to group reads in bins. We show that most reads from each bin belong to a single chromosome. CLAME is very effective recovering most of the reads belonging to the predominant species within a metagenome. Conclusions We developed a tool that can be used to extract genomes (or parts of them) from a complex metagenome. Electronic supplementary material The online version of this article (10.1186/s12864-018-5191-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andres Benavides
- Grupo SISTEMIC, Ingeniería Electrónica, Facultad de Ingeniería, Universidad de Antioquia UdeA, Calle 70 No, 52-21, Medellín, Colombia.
| | - Juan Pablo Isaza
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia UdeA, Calle 70 No, 52-21, Medellín, Colombia.,Grupo de Parasitología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No, 52-21, Medellín, Colombia
| | - Juan Pablo Niño-García
- Escuela de Microbiología, Universidad de Antioquia UdeA, Calle 70 No, 52-21, Medellín, Colombia
| | - Juan Fernando Alzate
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia UdeA, Calle 70 No, 52-21, Medellín, Colombia.,Grupo de Parasitología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No, 52-21, Medellín, Colombia
| | - Felipe Cabarcas
- Grupo SISTEMIC, Ingeniería Electrónica, Facultad de Ingeniería, Universidad de Antioquia UdeA, Calle 70 No, 52-21, Medellín, Colombia.,Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia UdeA, Calle 70 No, 52-21, Medellín, Colombia
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Krupovic M, Cvirkaite-Krupovic V, Iranzo J, Prangishvili D, Koonin EV. Viruses of archaea: Structural, functional, environmental and evolutionary genomics. Virus Res 2017; 244:181-193. [PMID: 29175107 DOI: 10.1016/j.virusres.2017.11.025] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 11/20/2017] [Accepted: 11/20/2017] [Indexed: 11/18/2022]
Abstract
Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among viruses of bacteria or eukaryotes. The uniqueness of the virion morphologies is matched by the distinctiveness of the genomes of these viruses, with ∼75% of genes encoding unique proteins, refractory to functional annotation based on sequence analyses. In this review, we summarize the state-of-the-art knowledge on various aspects of archaeal virus genomics. First, we outline how structural and functional genomics efforts provided valuable insights into the functions of viral proteins and revealed intricate details of the archaeal virus-host interactions. We then highlight recent metagenomics studies, which provided a glimpse at the diversity of uncultivated viruses associated with the ubiquitous archaea in the oceans, including Thaumarchaeota, Marine Group II Euryarchaeota, and others. These findings, combined with the recent discovery that archaeal viruses mediate a rapid turnover of thaumarchaea in the deep sea ecosystems, illuminate the prominent role of these viruses in the biosphere. Finally, we discuss the origins and evolution of archaeal viruses and emphasize the evolutionary relationships between viruses and non-viral mobile genetic elements. Further exploration of the archaeal virus diversity as well as functional studies on diverse virus-host systems are bound to uncover novel, unexpected facets of the archaeal virome.
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Affiliation(s)
- Mart Krupovic
- Department of Microbiology, Institut Pasteur, 25 rue du Dr. Roux, Paris 75015, Paris, France.
| | | | - Jaime Iranzo
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - David Prangishvili
- Department of Microbiology, Institut Pasteur, 25 rue du Dr. Roux, Paris 75015, Paris, France
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
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Abstract
One of the most prominent features of archaea is the extraordinary diversity of their DNA viruses. Many archaeal viruses differ substantially in morphology from bacterial and eukaryotic viruses and represent unique virus families. The distinct nature of archaeal viruses also extends to the gene composition and architectures of their genomes and the properties of the proteins that they encode. Environmental research has revealed prominent roles of archaeal viruses in influencing microbial communities in ocean ecosystems, and recent metagenomic studies have uncovered new groups of archaeal viruses that infect extremophiles and mesophiles in diverse habitats. In this Review, we summarize recent advances in our understanding of the genomic and morphological diversity of archaeal viruses and the molecular biology of their life cycles and virus-host interactions, including interactions with archaeal CRISPR-Cas systems. We also examine the potential origins and evolution of archaeal viruses and discuss their place in the global virosphere.
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Formation of a Viral Replication Focus in Sulfolobus Cells Infected by the Rudivirus Sulfolobus islandicus Rod-Shaped Virus 2. J Virol 2017; 91:JVI.00486-17. [PMID: 28424282 DOI: 10.1128/jvi.00486-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 04/11/2017] [Indexed: 01/05/2023] Open
Abstract
Viral factories are compartmentalized centers for viral replication and assembly in infected eukaryotic cells. Here, we report the formation of a replication focus by prototypical archaeal Sulfolobus islandicus rod-shaped virus 2 (SIRV2) in the model archaeon Sulfolobus This rod-shaped virus belongs to the viral family Rudiviridae, carrying linear double-stranded DNA (dsDNA) genomes, which are very common in geothermal environments. We demonstrate that SIRV2 DNA synthesis is confined to a focus near the periphery of infected cells. Moreover, viral and cellular replication proteins are recruited to, and concentrated in, the viral replication focus. Furthermore, we show that of the four host DNA polymerases (DNA polymerase I [Dpo1] to Dpo4), only Dpo1 participates in viral DNA synthesis. This constitutes the first report of the formation of a viral replication focus in archaeal cells, suggesting that organization of viral replication in foci is a widespread strategy employed by viruses of the three domains of life.IMPORTANCE The organization of viral replication in foci or viral factories has been mostly described for different eukaryotic viruses and for several bacteriophages. This work constitutes the first report of the formation of a viral replication center by a virus infecting members of the Archaea domain.
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DeCastro ME, Rodríguez-Belmonte E, González-Siso MI. Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes. Front Microbiol 2016; 7:1521. [PMID: 27729905 PMCID: PMC5037290 DOI: 10.3389/fmicb.2016.01521] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/12/2016] [Indexed: 11/24/2022] Open
Abstract
Microbial populations living in environments with temperatures above 50°C (thermophiles) have been widely studied, increasing our knowledge in the composition and function of these ecological communities. Since these populations express a broad number of heat-resistant enzymes (thermozymes), they also represent an important source for novel biocatalysts that can be potentially used in industrial processes. The integrated study of the whole-community DNA from an environment, known as metagenomics, coupled with the development of next generation sequencing (NGS) technologies, has allowed the generation of large amounts of data from thermophiles. In this review, we summarize the main approaches commonly utilized for assessing the taxonomic and functional diversity of thermophiles through metagenomics, including several bioinformatics tools and some metagenome-derived methods to isolate their thermozymes.
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Affiliation(s)
- María-Eugenia DeCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña A Coruña, Spain
| | - Esther Rodríguez-Belmonte
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña A Coruña, Spain
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña A Coruña, Spain
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Draft Genome Sequence of the Sulfolobales Archaeon AZ1, Obtained through Metagenomic Analysis of a Mexican Hot Spring. GENOME ANNOUNCEMENTS 2014; 2:2/2/e00164-14. [PMID: 24604657 PMCID: PMC3945513 DOI: 10.1128/genomea.00164-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The Sulfolobales archaea have been found inhabiting acidic hot springs all over the world. Here, we report the 1.798-Mbp draft genome sequence of the thermoacidophilic Sulfolobales archaeon AZ1, reconstructed from the metagenome of a Mexican hot spring. Sequence-based comparisons revealed that the Sulfolobales archaeon AZ1 represents a novel candidate genus.
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Bize A, Sezonov G, Prangishvili D. [Enigmatic archaeal viruses]. Biol Aujourdhui 2013; 207:169-79. [PMID: 24330970 DOI: 10.1051/jbio/2013015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Indexed: 11/14/2022]
Abstract
Viruses infecting microorganisms of the third domain of life, Archaea, are still poorly characterized: to date, only about fifty of these viruses have been isolated. Their hosts are hyperthermophilic, acidothermophilic, and extreme halophilic or methanogenic archaea. Their morphotypes are highly diverse and their gene content is very specific. Some of these viruses have developed extraordinary mechanisms to open the cell wall thanks to the formation of exceptional pyramidal nanostructures. The still limited knowledge about the biology of archaeoviruses should develop rapidly in the coming years.
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Affiliation(s)
| | - Guennadi Sezonov
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France - UMR 7138 Systématique, Adaptation, Évolution, Université Pierre et Marie Curie, 7 quai Saint Bernard, 75252 Paris Cedex 05, France
| | - David Prangishvili
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
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López-López O, Cerdán ME, González-Siso MI. Hot spring metagenomics. Life (Basel) 2013; 3:308-20. [PMID: 25369743 PMCID: PMC4187134 DOI: 10.3390/life3020308] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 04/11/2013] [Accepted: 04/15/2013] [Indexed: 12/14/2022] Open
Abstract
Hot springs have been investigated since the XIX century, but isolation and examination of their thermophilic microbial inhabitants did not start until the 1950s. Many thermophilic microorganisms and their viruses have since been discovered, although the real complexity of thermal communities was envisaged when research based on PCR amplification of the 16S rRNA genes arose. Thereafter, the possibility of cloning and sequencing the total environmental DNA, defined as metagenome, and the study of the genes rescued in the metagenomic libraries and assemblies made it possible to gain a more comprehensive understanding of microbial communities—their diversity, structure, the interactions existing between their components, and the factors shaping the nature of these communities. In the last decade, hot springs have been a source of thermophilic enzymes of industrial interest, encouraging further study of the poorly understood diversity of microbial life in these habitats.
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Affiliation(s)
- Olalla López-López
- Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain.
| | - María Esperanza Cerdán
- Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain.
| | - María Isabel González-Siso
- Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain.
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