1
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Bullen NP, Johnson CN, Andersen SE, Arya G, Marotta SR, Lee YJ, Weigele PR, Whitney JC, Duerkop BA. An enterococcal phage protein inhibits type IV restriction enzymes involved in antiphage defense. Nat Commun 2024; 15:6955. [PMID: 39138193 PMCID: PMC11322646 DOI: 10.1038/s41467-024-51346-1] [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: 12/05/2023] [Accepted: 08/05/2024] [Indexed: 08/15/2024] Open
Abstract
The prevalence of multidrug resistant (MDR) bacterial infections continues to rise as the development of antibiotics needed to combat these infections remains stagnant. MDR enterococci are a major contributor to this crisis. A potential therapeutic approach for combating MDR enterococci is bacteriophage (phage) therapy, which uses lytic viruses to infect and kill pathogenic bacteria. While phages that lyse some strains of MDR enterococci have been identified, other strains display high levels of resistance and the mechanisms underlying this resistance are poorly defined. Here, we use a CRISPR interference (CRISPRi) screen to identify a genetic locus found on a mobilizable plasmid from Enterococcus faecalis involved in phage resistance. This locus encodes a putative serine recombinase followed by a Type IV restriction enzyme (TIV-RE) that we show restricts the replication of phage phi47 in vancomycin-resistant E. faecalis. We further find that phi47 evolves to overcome restriction by acquiring a missense mutation in a TIV-RE inhibitor protein. We show that this inhibitor, termed type IV restriction inhibiting factor A (tifA), binds and inactivates diverse TIV-REs. Overall, our findings advance our understanding of phage defense in drug-resistant E. faecalis and provide mechanistic insight into how phages evolve to overcome antiphage defense systems.
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Affiliation(s)
- Nathan P Bullen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4L8, Canada
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Cydney N Johnson
- Department of Immunology and Microbiology, University of Colorado School-Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045, USA
| | - Shelby E Andersen
- Department of Immunology and Microbiology, University of Colorado School-Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045, USA
| | - Garima Arya
- Department of Immunology and Microbiology, University of Colorado School-Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045, USA
| | - Sonia R Marotta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4L8, Canada
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - Peter R Weigele
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - John C Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4L8, Canada.
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School-Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045, USA.
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Bullen NP, Johnson CN, Andersen SE, Arya G, Marotta SR, Lee YJ, Weigele PR, Whitney JC, Duerkop BA. An enterococcal phage protein broadly inhibits type IV restriction enzymes involved in antiphage defense. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.16.567456. [PMID: 38014348 PMCID: PMC10680825 DOI: 10.1101/2023.11.16.567456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The prevalence of multidrug resistant (MDR) bacterial infections continues to rise as the development of antibiotics needed to combat these infections remains stagnant. MDR enterococci are a major contributor to this crisis. A potential therapeutic approach for combating MDR enterococci is bacteriophage (phage) therapy, which uses lytic viruses to infect and kill pathogenic bacteria. While phages that lyse some strains of MDR enterococci have been identified, other strains display high levels of resistance and the mechanisms underlying this resistance are poorly defined. Here, we use a CRISPR interference (CRISPRi) screen to identify a genetic locus found on a mobilizable plasmid from Enterococcus faecalis involved in phage resistance. This locus encodes a putative serine recombinase followed by a Type IV restriction enzyme (TIV-RE) that we show restricts the replication of phage phi47 in E. faecalis. We further find that phi47 evolves to overcome restriction by acquiring a missense mutation in a TIV-RE inhibitor protein. We show that this inhibitor, termed type IV restriction inhibiting factor A (tifA), binds and inactivates diverse TIV-REs. Overall, our findings advance our understanding of phage defense in drug-resistant E. faecalis and provide mechanistic insight into how phages evolve to overcome antiphage defense systems.
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Affiliation(s)
- Nathan P. Bullen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8S 4L8
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Cydney N. Johnson
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
| | - Shelby E. Andersen
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
| | - Garima Arya
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
| | - Sonia R. Marotta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8S 4L8
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, MA, USA, 01938
| | - Peter R. Weigele
- Research Department, New England Biolabs, Ipswich, MA, USA, 01938
| | - John C. Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8S 4L8
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
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3
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Handa S, Biswas T, Chakraborty J, Ghosh G, Paul BG, Ghosh P. Structural Requirements for Reverse Transcription by a Diversity-generating Retroelement. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.23.563531. [PMID: 37961358 PMCID: PMC10634737 DOI: 10.1101/2023.10.23.563531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Diversity-generating retroelements (DGRs) create massive protein sequence variation in ecologically diverse microbes. Variation occurs during reverse transcription of a protein-encoding RNA template coupled to misincorporation at adenosines. In the prototypical Bordetella bacteriophage DGR, the template must be surrounded by upstream and downstream RNA segments for cDNA synthesis by the reverse transcriptase bRT and associated protein Avd. The function of the surrounding RNA was unknown. Cryo-EM revealed that this RNA enveloped bRT and lay over barrel-shaped Avd, forming an intimate ribonucleoprotein (RNP). An abundance of essential interactions between RNA structural elements and bRT-Avd precisely positioned an RNA homoduplex for initiation of cDNA synthesis by cis -priming. Our results explain how the surrounding RNA primes cDNA synthesis, promotes processivity, terminates polymerization, and strictly limits mutagenesis to select proteins through mechanisms that are likely conserved in DGRs from distant taxa.
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Yang B, Wang H, Kong J, Fang X. Long-term monitoring of ultratrace nucleic acids using tetrahedral nanostructure-based NgAgo on wearable microneedles. Nat Commun 2024; 15:1936. [PMID: 38431675 PMCID: PMC10908814 DOI: 10.1038/s41467-024-46215-w] [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: 11/08/2023] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Real-time and continuous monitoring of nucleic acid biomarkers with wearable devices holds potential for personal health management, especially in the context of pandemic surveillance or intensive care unit disease. However, achieving high sensitivity and long-term stability remains challenging. Here, we report a tetrahedral nanostructure-based Natronobacterium gregoryi Argonaute (NgAgo) for long-term stable monitoring of ultratrace unamplified nucleic acids (cell-free DNAs and RNAs) in vivo for sepsis on wearable device. This integrated wireless wearable consists of a flexible circuit board, a microneedle biosensor, and a stretchable epidermis patch with enrichment capability. We comprehensively investigate the recognition mechanism of nucleic acids by NgAgo/guide DNA and signal transformation within the Debye distance. In vivo experiments demonstrate the suitability for real-time monitoring of cell-free DNA and RNA with a sensitivity of 0.3 fM up to 14 days. These results provide a strategy for highly sensitive molecular recognition in vivo and for on-body detection of nucleic acid.
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Affiliation(s)
- Bin Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Haonan Wang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China.
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5
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Doré H, Eisenberg AR, Junkins EN, Leventhal GE, Ganesh A, Cordero OX, Paul BG, Valentine DL, O’Malley MA, Wilbanks EG. Targeted hypermutation of putative antigen sensors in multicellular bacteria. Proc Natl Acad Sci U S A 2024; 121:e2316469121. [PMID: 38354254 PMCID: PMC10907252 DOI: 10.1073/pnas.2316469121] [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: 09/29/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024] Open
Abstract
Diversity-generating retroelements (DGRs) are used by bacteria, archaea, and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evolution of these targeted genes. However, the function and benefits of DGR-diversified proteins in cellular hosts remain elusive. We find that 82% of DGRs from one of the major monophyletic lineages of DGR reverse transcriptases are encoded by multicellular bacteria, which often have two or more DGR loci in their genomes. Using the multicellular purple sulfur bacterium Thiohalocapsa sp. PB-PSB1 as an example, we characterized nine distinct DGR loci capable of generating 10282 different combinations of target proteins. With environmental metagenomes from individual Thiohalocapsa aggregates, we show that most of PB-PSB1's DGR target genes are diversified across its biogeographic range, with spatial heterogeneity in the diversity of each locus. In Thiohalocapsa PB-PSB1 and other bacteria hosting this lineage of cellular DGRs, the diversified target genes are associated with NACHT-domain anti-phage defenses and putative ternary conflict systems previously shown to be enriched in multicellular bacteria. We propose that these DGR-diversified targets act as antigen sensors that confer a form of adaptive immunity to their multicellular consortia, though this remains to be experimentally tested. These findings could have implications for understanding the evolution of multicellularity, as the NACHT-domain anti-phage systems and ternary systems share both domain homology and conceptual similarities with the innate immune and programmed cell death pathways of plants and metazoans.
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Affiliation(s)
- H. Doré
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA93106
| | - A. R. Eisenberg
- Department of Chemical Engineering, University of California, Santa Barbara, CA93106
| | - E. N. Junkins
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA93106
| | - G. E. Leventhal
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Anakha Ganesh
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA02543
| | - O. X. Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - B. G. Paul
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA02543
| | - D. L. Valentine
- Department of Earth Science, University of California, Santa Barbara, CA93106
- Marine Science Institute, University of California, Santa Barbara, CA93106
| | - M. A. O’Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA93106
- Department of Bioengineering, University of California, Santa Barbara, CA93106
| | - E. G. Wilbanks
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA93106
- Department of Bioengineering, University of California, Santa Barbara, CA93106
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6
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Pérez Castro S, Peredo EL, Mason OU, Vineis J, Bowen JL, Mortazavi B, Ganesh A, Ruff SE, Paul BG, Giblin AE, Cardon ZG. Diversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes. Appl Environ Microbiol 2023; 89:e0098823. [PMID: 37882526 PMCID: PMC10686091 DOI: 10.1128/aem.00988-23] [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] [Received: 06/14/2023] [Accepted: 09/04/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Salt marshes are known for their significant carbon storage capacity, and sulfur cycling is closely linked with the ecosystem-scale carbon cycling in these ecosystems. Sulfate reducers are key for the decomposition of organic matter, and sulfur oxidizers remove toxic sulfide, supporting the productivity of marsh plants. To date, the complexity of coastal environments, heterogeneity of the rhizosphere, high microbial diversity, and uncultured majority hindered our understanding of the genomic diversity of sulfur-cycling microbes in salt marshes. Here, we use comparative genomics to overcome these challenges and provide an in-depth characterization of sulfur-cycling microbial diversity in salt marshes. We characterize communities across distinct sites and plant species and uncover extensive genomic diversity at the taxon level and specific genomic features present in MAGs affiliated with uncultivated sulfur-cycling lineages. Our work provides insights into the partnerships in salt marshes and a roadmap for multiscale analyses of diversity in complex biological systems.
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Affiliation(s)
- Sherlynette Pérez Castro
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- Crop and Soil Sciences, University of Georgia, Athens, USA
| | - Elena L. Peredo
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Olivia U. Mason
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
| | - Joseph Vineis
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, Massachusetts, USA
| | - Jennifer L. Bowen
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, Massachusetts, USA
| | - Behzad Mortazavi
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, USA
| | - Anakha Ganesh
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - S. Emil Ruff
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Blair G. Paul
- Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Anne E. Giblin
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Zoe G. Cardon
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
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7
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Arkhipova IR, Yushenova IA. To Be Mobile or Not: The Variety of Reverse Transcriptases and Their Recruitment by Host Genomes. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1754-1762. [PMID: 38105196 DOI: 10.1134/s000629792311007x] [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: 09/13/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 12/19/2023]
Abstract
Reverse transcriptases (RT), or RNA-dependent DNA polymerases, are unorthodox enzymes that originally added a new angle to the conventional view of the unidirectional flow of genetic information in the cell from DNA to RNA to protein. First discovered in vertebrate retroviruses, RTs were since re-discovered in most eukaryotes, bacteria, and archaea, spanning essentially all domains of life. For retroviruses, RTs provide the ability to copy the RNA genome into DNA for subsequent incorporation into the host genome, which is essential for their replication and survival. In cellular organisms, most RT sequences originate from retrotransposons, the type of self-replicating genetic elements that rely on reverse transcription to copy and paste their sequences into new genomic locations. Some retroelements, however, can undergo domestication, eventually becoming a valuable addition to the overall repertoire of cellular enzymes. They can be beneficial yet accessory, like the diversity-generating elements, or even essential, like the telomerase reverse transcriptases. Nowadays, ever-increasing numbers of domesticated RT-carrying genetic elements are being discovered. It may be argued that domesticated RTs and reverse transcription in general is more widespread in cellular organisms than previously thought, and that many important cellular functions, such as chromosome end maintenance, may evolve from an originally selfish process of converting RNA into DNA.
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Affiliation(s)
- Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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8
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Medvedeva S, Borrel G, Krupovic M, Gribaldo S. A compendium of viruses from methanogenic archaea reveals their diversity and adaptations to the gut environment. Nat Microbiol 2023; 8:2170-2182. [PMID: 37749252 DOI: 10.1038/s41564-023-01485-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/30/2023] [Indexed: 09/27/2023]
Abstract
Methanogenic archaea are major producers of methane, a potent greenhouse gas and biofuel, and are widespread in diverse environments, including the animal gut. The ecophysiology of methanogens is likely impacted by viruses, which remain, however, largely uncharacterized. Here we carried out a global investigation of viruses associated with all current diversity of methanogens by assembling an extensive CRISPR database consisting of 156,000 spacers. We report 282 high-quality (pro)viral and 205 virus-like/plasmid sequences assigned to hosts belonging to ten main orders of methanogenic archaea. Viruses of methanogens can be classified into 87 families, underscoring a still largely undiscovered genetic diversity. Viruses infecting gut-associated archaea provide evidence of convergence in adaptation with viruses infecting gut-associated bacteria. These viruses contain a large repertoire of lysin proteins that cleave archaeal pseudomurein and are enriched in glycan-binding domains (Ig-like/Flg_new) and diversity-generating retroelements. The characterization of this vast repertoire of viruses paves the way towards a better understanding of their role in regulating methanogen communities globally, as well as the development of much-needed genetic tools.
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Affiliation(s)
- Sofia Medvedeva
- Institut Pasteur, Université Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Guillaume Borrel
- Institut Pasteur, Université Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Unit Archaeal Virology, Paris, France.
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
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9
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Liu J, Guo Y, Gu H, Liu Z, Hu X, Yu Z, Li Y, Li L, Sui Y, Jin J, Liu X, Adams JM, Wang G. Conversion of steppe to cropland increases spatial heterogeneity of soil functional genes. THE ISME JOURNAL 2023; 17:1872-1883. [PMID: 37607984 PMCID: PMC10579271 DOI: 10.1038/s41396-023-01496-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/24/2023]
Abstract
The microbiome function responses to land use change are important for the long-term prediction and management of soil ecological functions under human influence. However, it has remains uncertain how the biogeographic patterns of soil functional composition change when transitioning from natural steppe soils (NS) to agricultural soils (AS). We collected soil samples from adjacent pairs of AS and NS across 900 km of Mollisol areas in northeast China, and the soil functional composition was characterized using shotgun sequencing. AS had higher functional alpha-diversity indices with respect to KO trait richness and a higher Shannon index than NS. The distance-decay slopes of functional gene composition were steeper in AS than in NS along both spatial and environmental gradients. Land-use conversion from steppe to farmland diversified functional gene profiles both locally and spatially; it increased the abundances of functional genes related to labile carbon, but decreased those related to recalcitrant substrate mobilization (e.g., lignin), P cycling, and S cycling. The composition of gene functional traits was strongly driven by stochastic processes, while the degree of stochasticity was higher in NS than in AS, as revealed by the neutral community model and normalized stochasticity ratio analysis. Alpha-diversity of core functional genes was strongly related to multi-nutrient cycling in AS, suggesting a key relationship to soil fertility. The results of this study challenge the paradigm that the conversion of natural to agricultural habitat will homogenize soil properties and biology while reducing local and regional gene functional diversity.
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Affiliation(s)
- Junjie Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Yaping Guo
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, P R China
| | - Haidong Gu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Zhuxiu Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Xiaojing Hu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Zhenhua Yu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Yansheng Li
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Lujun Li
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Yueyu Sui
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Jian Jin
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Xiaobing Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China
| | - Jonathan M Adams
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, P R China.
| | - Guanghua Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, P R China.
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10
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Maatouk M, Rolain JM, Bittar F. Using Genomics to Decipher the Enigmatic Properties and Survival Adaptation of Candidate Phyla Radiation. Microorganisms 2023; 11:1231. [PMID: 37317205 DOI: 10.3390/microorganisms11051231] [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: 04/10/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 06/16/2023] Open
Abstract
Microbial ecology is a critical field for understanding the composition, diversity, and functions of microorganisms in various environmental and health-related processes. The discovery of Candidate Phyla Radiation (CPR) through culture-independent methods has introduced a new division of microbes characterized by a symbiotic/parasitic lifestyle, small cell size, and small genome. Despite being poorly understood, CPRs have garnered significant attention in recent years due to their widespread detection in a variety of environmental and clinical samples. These microorganisms have been found to exhibit a high degree of genetic diversity compared to other microbes. Several studies have shed light on their potential importance in global biogeochemical cycles and their impact on various human activities. In this review, we provide a systematic overview of the discovery of CPRs. We then focus on describing how the genomic characteristics of CPRs have helped them interact with and adapt to other microbes in different ecological niches. Future works should focus on discovering the metabolic capacities of CPRs and, if possible, isolating them to obtain a better understanding of these microorganisms.
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Affiliation(s)
- Mohamad Maatouk
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Jean-Marc Rolain
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Fadi Bittar
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
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11
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Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota. Nat Microbiol 2023; 8:727-744. [PMID: 36928026 PMCID: PMC10066038 DOI: 10.1038/s41564-022-01319-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 12/30/2022] [Indexed: 03/18/2023]
Abstract
Candidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. We analysed 72 newly sequenced and 349 existing Omnitrophota genomes representing 6 classes and 276 species, along with Earth Microbiome Project data to evaluate habitat, metabolic traits and lifestyles. We applied fluorescence-activated cell sorting and differential size filtration, and showed that most Omnitrophota are ultra-small (~0.2 μm) cells that are found in water, sediments and soils. Omnitrophota genomes in 6 classes are reduced, but maintain major biosynthetic and energy conservation pathways, including acetogenesis (with or without the Wood-Ljungdahl pathway) and diverse respirations. At least 64% of Omnitrophota genomes encode gene clusters typical of bacterial symbionts, suggesting host-associated lifestyles. We repurposed quantitative stable-isotope probing data from soils dominated by andesite, basalt or granite weathering and identified 3 families with high isotope uptake consistent with obligate bacterial predators. We propose that most Omnitrophota inhabit various ecosystems as predators or parasites.
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12
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Diversity-Generating Retroelements in Prokaryotic Immunity. Int J Mol Sci 2023; 24:ijms24065614. [PMID: 36982690 PMCID: PMC10053308 DOI: 10.3390/ijms24065614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
Adaptive immunity systems found in different organisms fall into two major types. Prokaryotes possess CRISPR-Cas systems that recognize former invaders using memorized (captured) pieces of their DNA as pathogen signatures. Mammals possess a vast repertoire of antibodies and T-cell receptor variants generated in advance. In this second type of adaptive immunity, a pathogen presentation to the immune system specifically activates the cells that express matching antibodies or receptors. These cells proliferate to fight the infection and form the immune memory. The principle of preemptive production of diverse defense proteins for future use can hypothetically take place in microbes too. We propose a hypothesis that prokaryotes employ diversity-generating retroelements to prepare defense proteins against yet-unknown invaders. In this study, we test this hypothesis with the methods of bioinformatics and identify several candidate defense systems based on diversity-generating retroelements.
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13
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Gios E, Mosley OE, Weaver L, Close M, Daughney C, Handley KM. Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles. ISME COMMUNICATIONS 2023; 3:13. [PMID: 36808147 PMCID: PMC9938205 DOI: 10.1038/s43705-023-00223-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 06/16/2023]
Abstract
Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) and DPANN radiation are characterized by ultra-small cell and genomes sizes, resulting in limited metabolic capacities and probable dependency on other organisms to survive. We applied a multi-omics approach to characterize the ultra-small microbial communities over a wide range of aquifer groundwater chemistries. Results expand the known global range of these unusual organisms, demonstrate the wide geographical range of over 11,000 subsurface-adapted Patescibacteria, Dependentiae and DPANN archaea, and indicate that prokaryotes with ultra-small genomes and minimalistic metabolism are a characteristic feature of the terrestrial subsurface. Community composition and metabolic activities were largely shaped by water oxygen content, while highly site-specific relative abundance profiles were driven by a combination of groundwater physicochemistries (pH, nitrate-N, dissolved organic carbon). We provide insights into the activity of ultra-small prokaryotes with evidence that they are major contributors to groundwater community transcriptional activity. Ultra-small prokaryotes exhibited genetic flexibility with respect to groundwater oxygen content, and transcriptionally distinct responses, including proportionally greater transcription invested into amino acid and lipid metabolism and signal transduction in oxic groundwater, along with differences in taxa transcriptionally active. Those associated with sediments differed from planktonic counterparts in species composition and transcriptional activity, and exhibited metabolic adaptations reflecting a surface-associated lifestyle. Finally, results showed that groups of phylogenetically diverse ultra-small organisms co-occurred strongly across sites, indicating shared preferences for groundwater conditions.
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Affiliation(s)
- Emilie Gios
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- NINA, Norwegian Institute for Nature Research, Trondheim, Norway
| | - Olivia E Mosley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- NatureMetrics Ltd, Surrey Research Park, Guildford, UK
| | - Louise Weaver
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Murray Close
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Chris Daughney
- GNS Science, Lower Hutt, New Zealand
- NIWA, National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Kim M Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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14
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Macadangdang BR, Makanani SK, Miller JF. Accelerated Evolution by Diversity-Generating Retroelements. Annu Rev Microbiol 2022; 76:389-411. [PMID: 35650669 DOI: 10.1146/annurev-micro-030322-040423] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Diversity-generating retroelements (DGRs) create vast amounts of targeted, functional diversity by facilitating the rapid evolution of ligand-binding protein domains. Thousands of DGRs have been identified in bacteria, archaea, and their respective viruses. They are broadly distributed throughout the microbial world, with enrichment observed in certain taxa and environments. The diversification machinery works through a novel mechanism termed mutagenic retrohoming, whereby nucleotide sequence information is copied from an invariant DNA template repeat (TR) into an RNA intermediate, selectively mutagenized at TR adenines during cDNA synthesis by a DGR-encoded reverse transcriptase, and transferred to a variable repeat (VR) region within a variable-protein gene (54). This unidirectional flow of information leaves TR-DNA sequences unmodified, allowing for repeated rounds of mutagenic retrohoming to optimize variable-protein function. DGR target genes are often modular and can encode one or more of a wide variety of discrete functional domains appended to a diversifiable ligand-binding motif. Bacterial variable proteins often localize to cell surfaces, although a subset appear to be cytoplasmic, while phage-encoded DGRs commonly diversify tail fiber-associated receptor-binding proteins. Here, we provide a comprehensive review of the mechanism and consequences of accelerated protein evolution by these unique and beneficial genetic elements. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Benjamin R Macadangdang
- Division of Neonatology and Developmental Biology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, California, USA; .,California NanoSystems Institute, University of California, Los Angeles, California, USA
| | - Sara K Makanani
- California NanoSystems Institute, University of California, Los Angeles, California, USA.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; .,Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA;
| | - Jeff F Miller
- California NanoSystems Institute, University of California, Los Angeles, California, USA.,Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA; .,Molecular Biology Institute, University of California, Los Angeles, California, USA
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15
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Shu WS, Huang LN. Microbial diversity in extreme environments. Nat Rev Microbiol 2022; 20:219-235. [PMID: 34754082 DOI: 10.1038/s41579-021-00648-y] [Citation(s) in RCA: 126] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.
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Affiliation(s)
- Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
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16
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Benler S, Koonin EV. Recruitment of Mobile Genetic Elements for Diverse Cellular Functions in Prokaryotes. Front Mol Biosci 2022; 9:821197. [PMID: 35402511 PMCID: PMC8987985 DOI: 10.3389/fmolb.2022.821197] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/08/2022] [Indexed: 12/15/2022] Open
Abstract
Prokaryotic genomes are replete with mobile genetic elements (MGE) that span a continuum of replication autonomy. On numerous occasions during microbial evolution, diverse MGE lose their autonomy altogether but, rather than being quickly purged from the host genome, assume a new function that benefits the host, rendering the immobilized MGE subject to purifying selection, and resulting in its vertical inheritance. This mini-review highlights the diversity of the repurposed (exapted) MGE as well as the plethora of cellular functions that they perform. The principal contribution of the exaptation of MGE and their components is to the prokaryotic functional systems involved in biological conflicts, and in particular, defense against viruses and other MGE. This evolutionary entanglement between MGE and defense systems appears to stem both from mechanistic similarities and from similar evolutionary predicaments whereby both MGEs and defense systems tend to incur fitness costs to the hosts and thereby evolve mechanisms for survival including horizontal mobility, causing host addiction, and exaptation for functions beneficial to the host. The examples discussed demonstrate that the identity of an MGE, overall mobility and relationship with the host cell (mutualistic, symbiotic, commensal, or parasitic) are all factors that affect exaptation.
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Affiliation(s)
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
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17
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Paul BG, Eren AM. Eco-evolutionary significance of domesticated retroelements in microbial genomes. Mob DNA 2022; 13:6. [PMID: 35197094 PMCID: PMC8867640 DOI: 10.1186/s13100-022-00262-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/03/2022] [Indexed: 01/03/2023] Open
Abstract
Since the first discovery of reverse transcriptase in bacteria, and later in archaea, bacterial and archaeal retroelements have been defined by their common enzyme that coordinates diverse functions. Yet, evolutionary refinement has produced distinct retroelements across the tree of microbial life that are perhaps best described in terms of their programmed RNA-a compact sequence that preserves core information for a sophisticated mechanism. From this perspective, reverse transcriptase has been selected as the modular tool for carrying out nature's instructions in various RNA templates. Beneficial retroelements-those that can provide a fitness advantage to their host-evolved to their extant forms in a wide array of microorganisms and their viruses, spanning nearly all habitats. Within each specialized retroelement class, several universal features seem to be shared across diverse taxa, while specific functional and mechanistic insights are based on only a few model retroelement systems from clinical isolates. Currently, little is known about the diversity of cellular functions and ecological significance of retroelements across different biomes. With increasing availability of isolate, metagenome-assembled, and single-amplified genomes, the taxonomic and functional breadth of prokaryotic retroelements is coming into clearer view. This review explores the recently characterized classes of beneficial, yet accessory retroelements of bacteria and archaea. We describe how these specialized mechanisms exploit a form of fixed mobility, whereby the retroelements do not appear to proliferate selfishly throughout the genome. Moreover, we discuss computational approaches for systematic identification of retroelements from vast sequence repositories and highlight recent discoveries in terms of their apparent distribution and ecological significance in nature. Lastly, we present a new perspective on the eco-evolutionary significance of these genetic elements in marine bacteria and demonstrate approaches that enable the characterization of their environmental diversity through metagenomics.
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Affiliation(s)
- Blair G Paul
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, USA.
| | - A Murat Eren
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, MA, USA.
- Department of Medicine, University of Chicago, Chicago, IL, USA.
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18
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González-Delgado A, Mestre MR, Martínez-Abarca F, Toro N. Prokaryotic reverse transcriptases: from retroelements to specialized defense systems. FEMS Microbiol Rev 2021; 45:fuab025. [PMID: 33983378 PMCID: PMC8632793 DOI: 10.1093/femsre/fuab025] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/07/2021] [Indexed: 12/30/2022] Open
Abstract
Reverse transcriptases (RTs) catalyze the polymerization of DNA from an RNA template. These enzymes were first discovered in RNA tumor viruses in 1970, but it was not until 1989 that they were found in prokaryotes as a key component of retrons. Apart from RTs encoded by the 'selfish' mobile retroelements known as group II introns, prokaryotic RTs are extraordinarily diverse, but their function has remained elusive. However, recent studies have revealed that different lineages of prokaryotic RTs, including retrons, those associated with CRISPR-Cas systems, Abi-like RTs and other yet uncharacterized RTs, are key components of different lines of defense against phages and other mobile genetic elements. Prokaryotic RTs participate in various antiviral strategies, including abortive infection (Abi), in which the infected cell is induced to commit suicide to protect the host population, adaptive immunity, in which a memory of previous infection is used to build an efficient defense, and other as yet unidentified mechanisms. These prokaryotic enzymes are attracting considerable attention, both for use in cutting-edge technologies, such as genome editing, and as an emerging research topic. In this review, we discuss what is known about prokaryotic RTs, and the exciting evidence for their domestication from retroelements to create specialized defense systems.
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Affiliation(s)
- Alejandro González-Delgado
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Mario Rodríguez Mestre
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, C/ Profesor Albareda 1, 18008 Granada, Spain
- Department of Biochemistry, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas “Alberto Sols”, CSIC-UAM, Madrid, Spain
| | - Francisco Martínez-Abarca
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Nicolás Toro
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, C/ Profesor Albareda 1, 18008 Granada, Spain
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19
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Egido JE, Costa AR, Aparicio-Maldonado C, Haas PJ, Brouns SJJ. Mechanisms and clinical importance of bacteriophage resistance. FEMS Microbiol Rev 2021; 46:6374866. [PMID: 34558600 PMCID: PMC8829019 DOI: 10.1093/femsre/fuab048] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/15/2021] [Indexed: 12/24/2022] Open
Abstract
We are in the midst of a golden age of uncovering defense systems against bacteriophages. Apart from the fundamental interest in these defense systems, and revolutionary applications that have been derived from them (e.g. CRISPR-Cas9 and restriction endonucleases), it is unknown how defense systems contribute to resistance formation against bacteriophages in clinical settings. Bacteriophages are now being reconsidered as therapeutic agents against bacterial infections due the emergence of multidrug resistance. However, bacteriophage resistance through defense systems and other means could hinder the development of successful phage-based therapies. Here, we review the current state of the field of bacteriophage defense, highlight the relevance of bacteriophage defense for potential clinical use of bacteriophages as therapeutic agents and suggest new directions of research.
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Affiliation(s)
- Julia E Egido
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands.,Fagenbank, Delft, Netherlands
| | - Cristian Aparicio-Maldonado
- Department of Bionanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands
| | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584 CX Utrecht, Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, Netherlands.,Kavli Institute of Nanoscience, Delft, Netherlands.,Fagenbank, Delft, Netherlands
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20
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Huang WC, Liu Y, Zhang X, Zhang CJ, Zou D, Zheng S, Xu W, Luo Z, Liu F, Li M. Comparative genomic analysis reveals metabolic flexibility of Woesearchaeota. Nat Commun 2021; 12:5281. [PMID: 34489402 PMCID: PMC8421398 DOI: 10.1038/s41467-021-25565-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 08/12/2021] [Indexed: 02/08/2023] Open
Abstract
The archaeal phylum Woesearchaeota, within the DPANN superphylum, includes phylogenetically diverse microorganisms that inhabit various environments. Their biology is poorly understood due to the lack of cultured isolates. Here, we analyze datasets of Woesearchaeota 16S rRNA gene sequences and metagenome-assembled genomes to infer global distribution patterns, ecological preferences and metabolic capabilities. Phylogenomic analyses indicate that the phylum can be classified into ten subgroups, termed A-J. While a symbiotic lifestyle is predicted for most, some members of subgroup J might be host-independent. The genomes of several Woesearchaeota, including subgroup J, encode putative [FeFe] hydrogenases (known to be important for fermentation in other organisms), suggesting that these archaea might be anaerobic fermentative heterotrophs.
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Affiliation(s)
- Wen-Cong Huang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yang Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Xinxu Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Cui-Jing Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Dayu Zou
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Shiling Zheng
- Key Laboratory of Coastal Biology and Biological Resources Utilization, CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- School of Marine Sciences, Nanjing University of Information Science & Technology, Nanjing, China
| | - Fanghua Liu
- Key Laboratory of Coastal Biology and Biological Resources Utilization, CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
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21
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Suominen S, Dombrowski N, Sinninghe Damsté JS, Villanueva L. A diverse uncultivated microbial community is responsible for organic matter degradation in the Black Sea sulphidic zone. Environ Microbiol 2021; 23:2709-2728. [PMID: 31858660 PMCID: PMC8359207 DOI: 10.1111/1462-2920.14902] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 11/27/2022]
Abstract
Organic matter degradation in marine environments is essential for the recycling of nutrients, especially under conditions of anoxia where organic matter tends to accumulate. However, little is known about the diversity of the microbial communities responsible for the mineralization of organic matter in the absence of oxygen, as well as the factors controlling their activities. Here, we determined the active heterotrophic prokaryotic community in the sulphidic water column of the Black Sea, an ideal model system, where a tight coupling between carbon, nitrogen and sulphur cycles is expected. Active microorganisms degrading both dissolved organic matter (DOM) and protein extracts were determined using quantitative DNA stable isotope probing incubation experiments. These results were compared with the metabolic potential of metagenome-assembled genomes obtained from the water column. Organic matter incubations showed that groups like Cloacimonetes and Marinimicrobia are generalists degrading DOM. Based on metagenomic profiles the degradation proceeds in a potential interaction with members of the Deltaproteobacteria and Chloroflexi Dehalococcoidia. On the other hand, microbes with small genomes like the bacterial phyla Parcubacteria, Omnitrophica and of the archaeal phylum Woesearchaeota, were the most active, especially in protein-amended incubations, revealing the potential advantage of streamlined microorganisms in highly reduced conditions.
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Affiliation(s)
- Saara Suominen
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen HoornThe Netherlands
| | - Nina Dombrowski
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen HoornThe Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen HoornThe Netherlands
- Department of Earth Sciences, Faculty of GeosciencesUtrecht UniversityUtrechtThe Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen HoornThe Netherlands
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22
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Roux S, Paul BG, Bagby SC, Nayfach S, Allen MA, Attwood G, Cavicchioli R, Chistoserdova L, Gruninger RJ, Hallam SJ, Hernandez ME, Hess M, Liu WT, McAllister TA, O'Malley MA, Peng X, Rich VI, Saleska SR, Eloe-Fadrosh EA. Ecology and molecular targets of hypermutation in the global microbiome. Nat Commun 2021; 12:3076. [PMID: 34031405 PMCID: PMC8144416 DOI: 10.1038/s41467-021-23402-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/27/2021] [Indexed: 02/04/2023] Open
Abstract
Changes in the sequence of an organism's genome, i.e., mutations, are the raw material of evolution. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as diversity-generating retroelements (DGRs). DGRs have been characterized from cultivated bacteria and bacteriophages, and perform error-prone reverse transcription leading to mutations being introduced in specific target genes. DGR loci were also identified in several metagenomes, but the ecological roles and evolutionary drivers of these DGRs remain poorly understood. Here, we analyze a dataset of >30,000 DGRs from public metagenomes, establish six major lineages of DGRs including three primarily encoded by phages and seemingly used to diversify host attachment proteins, and demonstrate that DGRs are broadly active and responsible for >10% of all amino acid changes in some organisms. Overall, these results highlight the constraints under which DGRs evolve, and elucidate several distinct roles these elements play in natural communities.
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Affiliation(s)
- Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Blair G Paul
- Marine Biological Laboratory, Woods Hole, MA, USA
| | - Sarah C Bagby
- Department of Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Stephen Nayfach
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Graeme Attwood
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | | | | | - Robert J Gruninger
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, Canada
| | - Maria E Hernandez
- Instituto de Ecología A.C. Red de Manejo Biotechnológico de Recursos. Xalapa, Veracruz, México
| | | | - Wen-Tso Liu
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Xuefeng Peng
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, USA
| | | | | | - Emiley A Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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23
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Fones EM, Colman DR, Kraus EA, Stepanauskas R, Templeton AS, Spear JR, Boyd ES. Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation. THE ISME JOURNAL 2021; 15:1121-1135. [PMID: 33257813 PMCID: PMC8115248 DOI: 10.1038/s41396-020-00838-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/28/2020] [Accepted: 11/11/2020] [Indexed: 01/29/2023]
Abstract
Metagenome assembled genomes (MAGs) and single amplified genomes (SAGs) affiliated with two distinct Methanobacterium lineages were recovered from subsurface fracture waters of the Samail Ophiolite, Sultanate of Oman. Lineage Type I was abundant in waters with circumneutral pH, whereas lineage Type II was abundant in hydrogen rich, hyperalkaline waters. Type I encoded proteins to couple hydrogen oxidation to CO2 reduction, typical of hydrogenotrophic methanogens. Surprisingly, Type II, which branched from the Type I lineage, lacked homologs of two key oxidative [NiFe]-hydrogenases. These functions were presumably replaced by formate dehydrogenases that oxidize formate to yield reductant and cytoplasmic CO2 via a pathway that was unique among characterized Methanobacteria, allowing cells to overcome CO2/oxidant limitation in high pH waters. This prediction was supported by microcosm-based radiotracer experiments that showed significant biological methane generation from formate, but not bicarbonate, in waters where the Type II lineage was detected in highest relative abundance. Phylogenetic analyses and variability in gene content suggested that recent and ongoing diversification of the Type II lineage was enabled by gene transfer, loss, and transposition. These data indicate that selection imposed by CO2/oxidant availability drove recent methanogen diversification into hyperalkaline waters that are heavily impacted by serpentinization.
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Affiliation(s)
- Elizabeth M. Fones
- grid.41891.350000 0001 2156 6108Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717 USA
| | - Daniel R. Colman
- grid.41891.350000 0001 2156 6108Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717 USA
| | - Emily A. Kraus
- grid.254549.b0000 0004 1936 8155Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO 80401 USA
| | - Ramunas Stepanauskas
- grid.296275.d0000 0000 9516 4913Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544 USA
| | - Alexis S. Templeton
- grid.266190.a0000000096214564Department of Geological Sciences, University of Colorado, Boulder, CO 80309 USA
| | - John R. Spear
- grid.254549.b0000 0004 1936 8155Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO 80401 USA
| | - Eric S. Boyd
- grid.41891.350000 0001 2156 6108Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717 USA
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Handa S, Reyna A, Wiryaman T, Ghosh P. Determinants of adenine-mutagenesis in diversity-generating retroelements. Nucleic Acids Res 2021; 49:1033-1045. [PMID: 33367793 PMCID: PMC7826257 DOI: 10.1093/nar/gkaa1240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 02/01/2023] Open
Abstract
Diversity-generating retroelements (DGRs) vary protein sequences to the greatest extent known in the natural world. These elements are encoded by constituents of the human microbiome and the microbial ‘dark matter’. Variation occurs through adenine-mutagenesis, in which genetic information in RNA is reverse transcribed faithfully to cDNA for all template bases but adenine. We investigated the determinants of adenine-mutagenesis in the prototypical Bordetella bacteriophage DGR through an in vitro system composed of the reverse transcriptase bRT, Avd protein, and a specific RNA. We found that the catalytic efficiency for correct incorporation during reverse transcription by the bRT-Avd complex was strikingly low for all template bases, with the lowest occurring for adenine. Misincorporation across a template adenine was only somewhat lower in efficiency than correct incorporation. We found that the C6, but not the N1 or C2, purine substituent was a key determinant of adenine-mutagenesis. bRT-Avd was insensitive to the C6 amine of adenine but recognized the C6 carbonyl of guanine. We also identified two bRT amino acids predicted to nonspecifically contact incoming dNTPs, R74 and I181, as promoters of adenine-mutagenesis. Our results suggest that the overall low catalytic efficiency of bRT-Avd is intimately tied to its ability to carry out adenine-mutagenesis.
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Affiliation(s)
- Sumit Handa
- Department of Chemistry & Biochemistry, 9500 Gilman Drive, La Jolla, CA, 92093-0375, USA
| | - Andres Reyna
- Department of Chemistry & Biochemistry, 9500 Gilman Drive, La Jolla, CA, 92093-0375, USA
| | - Timothy Wiryaman
- Department of Chemistry & Biochemistry, 9500 Gilman Drive, La Jolla, CA, 92093-0375, USA
| | - Partho Ghosh
- Department of Chemistry & Biochemistry, 9500 Gilman Drive, La Jolla, CA, 92093-0375, USA
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López-García P, Moreira D. Physical connections: prokaryotes parasitizing their kin. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:54-61. [PMID: 33225570 DOI: 10.1111/1758-2229.12910] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 06/11/2023]
Affiliation(s)
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Orsay, AgroParisTech, 91400, France
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26
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Liu X, Wang Y, Gu JD. Ecological distribution and potential roles of Woesearchaeota in anaerobic biogeochemical cycling unveiled by genomic analysis. Comput Struct Biotechnol J 2021; 19:794-800. [PMID: 33552450 PMCID: PMC7844129 DOI: 10.1016/j.csbj.2021.01.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/21/2022] Open
Abstract
Woesearchaeota as a newly established member of the superphylum DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) are surprisingly abundant and diverse in a wide variety of environments, including deep oil reservoir, sulfuric springs and anoxic aquifers, indicating a high diversity of their roles in global biogeochemical cycles. However, ecological functions of them remain elusive. To fill up this gap, we analyzed and compared the global distribution patterns of Woesearchaeota using the genomes available publicly. As a result, both ecological distribution patterns and metabolic predictions support a key role of woesearchaeotal lineages in cycling of carbon, nitrogen, and sulfur. Multivariate regression analysis reveals that Woesearchaeota might function in consortium with methanogens in the cycling of carbon in anaerobic environments, particularly in soils or sediments. Moreover, comparative genomic analysis and ecological distribution suggest the potential roles of Woesearchaeota in the processes of denitrification, nitrogen fixation, and dissimilatory nitrite reduction, especially in the wastewater treatment systems; and also uncovered the potential capability of sulfate reduction, sulfide oxidation and thiosulfate oxidation in sulfuric or sulfidic-rich environments. Our findings add more information into the ecological roles of archaea in the anoxic environment.
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Affiliation(s)
- Xiaobo Liu
- Environmental Engineering Program, Guangdong Technion-Israel Institute of Technology (GTIIT), 241 Daxue Road, Shantou 515063, Guangdong, China
| | - Yali Wang
- Conservation Center, Guangdong Museum, 2 Zhujiang East Road, Tianhe District, Guangzhou 510623, Guangdong, China
| | - Ji-Dong Gu
- Environmental Engineering Program, Guangdong Technion-Israel Institute of Technology (GTIIT), 241 Daxue Road, Shantou 515063, Guangdong, China
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27
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Vallota-Eastman A, Arrington EC, Meeken S, Roux S, Dasari K, Rosen S, Miller JF, Valentine DL, Paul BG. Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria. BMC Genomics 2020; 21:664. [PMID: 32977771 PMCID: PMC7517822 DOI: 10.1186/s12864-020-07052-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/03/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Cyanobacteria maintain extensive repertoires of regulatory genes that are vital for adaptation to environmental stress. Some cyanobacterial genomes have been noted to encode diversity-generating retroelements (DGRs), which promote protein hypervariation through localized retrohoming and codon rewriting in target genes. Past research has shown DGRs to mainly diversify proteins involved in cell-cell attachment or viral-host attachment within viral, bacterial, and archaeal lineages. However, these elements may be critical in driving variation for proteins involved in other core cellular processes. RESULTS Members of 31 cyanobacterial genera encode at least one DGR, and together, their retroelements form a monophyletic clade of closely-related reverse transcriptases. This class of retroelements diversifies target proteins with unique domain architectures: modular ligand-binding domains often paired with a second domain that is linked to signal response or regulation. Comparative analysis indicates recent intragenomic duplication of DGR targets as paralogs, but also apparent intergenomic exchange of DGR components. The prevalence of DGRs and the paralogs of their targets is disproportionately high among colonial and filamentous strains of cyanobacteria. CONCLUSION We find that colonial and filamentous cyanobacteria have recruited DGRs to optimize a ligand-binding module for apparent function in signal response or regulation. These represent a unique class of hypervariable proteins, which might offer cyanobacteria a form of plasticity to adapt to environmental stress. This analysis supports the hypothesis that DGR-driven mutation modulates signaling and regulatory networks in cyanobacteria, suggestive of a new framework for the utility of localized genetic hypervariation.
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Affiliation(s)
- Alec Vallota-Eastman
- Interdepartmental Graduate Program for Marine Science, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Eleanor C Arrington
- Interdepartmental Graduate Program for Marine Science, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Siobhan Meeken
- Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL St, Woods Hole, MA, 02543, USA
| | - Simon Roux
- DOE Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Krishna Dasari
- Research Mentorship Program (RMP), University of California, Santa Barbara, CA, 93106, USA
| | - Sydney Rosen
- Research Mentorship Program (RMP), University of California, Santa Barbara, CA, 93106, USA
| | - Jeff F Miller
- Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - David L Valentine
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Earth Science, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Blair G Paul
- Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL St, Woods Hole, MA, 02543, USA.
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28
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Wong HL, MacLeod FI, White RA, Visscher PT, Burns BP. Microbial dark matter filling the niche in hypersaline microbial mats. MICROBIOME 2020; 8:135. [PMID: 32938503 PMCID: PMC7495880 DOI: 10.1186/s40168-020-00910-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/19/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Shark Bay, Australia, harbours one of the most extensive and diverse systems of living microbial mats that are proposed to be analogs of some of the earliest ecosystems on Earth. These ecosystems have been shown to possess a substantial abundance of uncultivable microorganisms. These enigmatic microbes, jointly coined as 'microbial dark matter' (MDM), are hypothesised to play key roles in modern microbial mats. RESULTS We reconstructed 115 metagenome-assembled genomes (MAGs) affiliated to MDM, spanning 42 phyla. This study reports for the first time novel microorganisms (Zixibacterial order GN15) putatively taking part in dissimilatory sulfate reduction in surface hypersaline settings, as well as novel eukaryote signature proteins in the Asgard archaea. Despite possessing reduced-size genomes, the MDM MAGs are capable of fermenting and degrading organic carbon, suggesting a role in recycling organic carbon. Several forms of RuBisCo were identified, allowing putative CO2 incorporation into nucleotide salvaging pathways, which may act as an alternative carbon and phosphorus source. High capacity of hydrogen production was found among Shark Bay MDM. Putative schizorhodopsins were also identified in Parcubacteria, Asgard archaea, DPANN archaea, and Bathyarchaeota, allowing these members to potentially capture light energy. Diversity-generating retroelements were prominent in DPANN archaea that likely facilitate the adaptation to a dynamic, host-dependent lifestyle. CONCLUSIONS This is the first study to reconstruct and describe in detail metagenome-assembled genomes (MAGs) affiliated with microbial dark matter in hypersaline microbial mats. Our data suggests that these microbial groups are major players in these systems. In light of our findings, we propose H2, ribose and CO/CO2 as the main energy currencies of the MDM community in these mat systems. Video Abstract.
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Affiliation(s)
- Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
| | - Fraser I MacLeod
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
| | - Richard Allen White
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
- RAW Molecular Systems LLC, Spokane, WA, USA
- Department of Bioinformatics and Genomics, The University of North Carolina, Charlotte, NC, USA
| | - Pieter T Visscher
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
- Department of Marine Sciences, University of Connecticut, Mansfield, USA
- Biogeosciences, the Université de Bourgogne Franche-Comté, Dijon, France
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia.
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29
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Cullings K, Stott MB, Marinkovich N, DeSimone J, Bhardwaj S. Phylum-level diversity of the microbiome of the extremophilic basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert: An island of biodiversity in a thermal soil desert. Microbiologyopen 2020; 9:e1062. [PMID: 32478485 PMCID: PMC7424252 DOI: 10.1002/mbo3.1062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 11/16/2022] Open
Abstract
We used high‐throughput DNA sequencing methods combined with bio‐geochemical profiles to characterize the internal environment and community structure of the microbiome of the basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert from soils within a geothermal feature of Yellowstone National Park. Pisolithus arhizus is unique in that it forms closed fruiting bodies that sequester visible sulfur within. Fourier transform infrared spectroscopy (FTIR) analysis demonstrates that the P. arhizus fruiting body also concentrates copper, manganese, nickel, and zinc and contains pure granular silica. Gas chromatography‐mass spectrometry (GC‐MS) analysis indicates an environment rich in hydrocarbons. Oxygen probe analysis reveals that zones of up to 4× atmospheric oxygen exist within nanometers of zones of near anoxia. Analysis of microbial community structure using high‐throughput DNA sequencing methods shows that the fruiting body supports a microbiome that reflects the physiochemical environment of the fruiting body. Diversity and richness measures indicate a microbiome that is significantly richer and more diverse than that of the soils in which P. arhizus grows. Further, P. arhizus sporocarps are enriched significantly in Proteobacteria (primarily Burkholderia) Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Nitrospirae, Elusimicrobia, and Latescibacteria (WS3) while soils are enriched in Actinobacteria (primarily Mycobacterium), Dormibacteraeota (AD3), and Eremiobacteraeota (WPS‐2). Finally, pairwise % similarity comparisons indicate that P. arhizus harbors two lineages that may represent new groups in the candidate phylum radiation (CPR). Together, these results demonstrate that P. arhizus provides a novel environment for microbiome studies and provides for interesting hypotheses regarding the evolution, origins, and functions of symbioses and novel microbes.
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Affiliation(s)
- Ken Cullings
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Julia DeSimone
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
| | - Shilpa Bhardwaj
- JQ Division, NASA-Ames Research Center, Moffett Field, California, USA
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30
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Morozova V, Fofanov M, Tikunova N, Babkin I, Morozov VV, Tikunov A. First crAss-Like Phage Genome Encoding the Diversity-Generating Retroelement (DGR). Viruses 2020; 12:v12050573. [PMID: 32456083 PMCID: PMC7290462 DOI: 10.3390/v12050573] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 12/20/2022] Open
Abstract
A new crAss-like genome encoding diversity-generating retroelement (DGR) was found in the fecal virome of a healthy volunteer. The genome of the phage referred to as the crAssphage LMMB, belonged to the candidate genus I of the AlphacrAssvirinae subfamily. The DGR-cassette of the crAssphage LMMB contained all the essential elements: the gene encoding reverse transcriptase (RT), the target gene (TG) encoding the tail-collar fiber protein, and variable and template repeats (VR and TR) with IMH (initiation of mutagenic homing) and IMH* sequences at the 3′-end of the VR and TR, respectively. Architecture of the DGR-cassette was TG-VR(IMH)-TR(IMH*)-RT and an accessory variable determinant (avd) was absent from the cassette. Analysis of 91 genomes and genome fragments from genus I of the AlphacrAssvirinae showed that 15 (16%) of the genomes had DGRs with the same architecture as the crAssphage LMMB, while 66 of the genomes contained incomplete DGR-cassettes or some elements of the DGR.
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31
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Simon AJ, Ellington AD, Finkelstein IJ. Retrons and their applications in genome engineering. Nucleic Acids Res 2020; 47:11007-11019. [PMID: 31598685 PMCID: PMC6868368 DOI: 10.1093/nar/gkz865] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/19/2019] [Accepted: 10/02/2019] [Indexed: 11/14/2022] Open
Abstract
Precision genome editing technologies have transformed modern biology. These technologies have arisen from the redirection of natural biological machinery, such as bacteriophage lambda proteins for recombineering and CRISPR nucleases for eliciting site-specific double-strand breaks. Less well-known is a widely distributed class of bacterial retroelements, retrons, that employ specialized reverse transcriptases to produce noncoding intracellular DNAs. Retrons' natural function and mechanism of genetic transmission have remained enigmatic. However, recent studies have harnessed their ability to produce DNA in situ for genome editing and evolution. This review describes retron biology and function in both natural and synthetic contexts. We also highlight areas that require further study to advance retron-based precision genome editing platforms.
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Affiliation(s)
- Anna J Simon
- Center for Systems and Synthetic Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ilya J Finkelstein
- Center for Systems and Synthetic Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
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32
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Nawrocki EP, Jones TA, Eddy SR. Group I introns are widespread in archaea. Nucleic Acids Res 2019; 46:7970-7976. [PMID: 29788499 PMCID: PMC6125680 DOI: 10.1093/nar/gky414] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 05/04/2018] [Indexed: 01/28/2023] Open
Abstract
Group I catalytic introns have been found in bacterial, viral, organellar, and some eukaryotic genomes, but not in archaea. All known archaeal introns are bulge-helix-bulge (BHB) introns, with the exception of a few group II introns. It has been proposed that BHB introns arose from extinct group I intron ancestors, much like eukaryotic spliceosomal introns are thought to have descended from group II introns. However, group I introns have little sequence conservation, making them difficult to detect with standard sequence similarity searches. Taking advantage of recent improvements in a computational homology search method that accounts for both conserved sequence and RNA secondary structure, we have identified 39 group I introns in a wide range of archaeal phyla, including examples of group I introns and BHB introns in the same host gene.
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Affiliation(s)
- Eric P Nawrocki
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD 20894, USA
| | - Thomas A Jones
- Howard Hughes Medical Institute, Harvard University, Cambridge, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA
| | - Sean R Eddy
- Howard Hughes Medical Institute, Harvard University, Cambridge, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA.,School of Engineering and Applied Sciences, Harvard University, Cambridge, USA
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Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nat Rev Microbiol 2019; 16:629-645. [PMID: 30181663 DOI: 10.1038/s41579-018-0076-2] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Candidate phyla radiation (CPR) bacteria and DPANN (an acronym of the names of the first included phyla) archaea are massive radiations of organisms that are widely distributed across Earth's environments, yet we know little about them. Initial indications are that they are consistently distinct from essentially all other bacteria and archaea owing to their small cell and genome sizes, limited metabolic capacities and often episymbiotic associations with other bacteria and archaea. In this Analysis, we investigate their biology and variations in metabolic capacities by analysis of approximately 1,000 genomes reconstructed from several metagenomics-based studies. We find that they are not monolithic in terms of metabolism but rather harbour a diversity of capacities consistent with a range of lifestyles and degrees of dependence on other organisms. Notably, however, certain CPR and DPANN groups seem to have exceedingly minimal biosynthetic capacities, whereas others could potentially be free living. Understanding of these microorganisms is important from the perspective of evolutionary studies and because their interactions with other organisms are likely to shape natural microbiome function.
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Handa S, Jiang Y, Tao S, Foreman R, Schinazi RF, Miller JF, Ghosh P. Template-assisted synthesis of adenine-mutagenized cDNA by a retroelement protein complex. Nucleic Acids Res 2019; 46:9711-9725. [PMID: 30007279 PMCID: PMC6182149 DOI: 10.1093/nar/gky620] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/27/2018] [Indexed: 12/28/2022] Open
Abstract
Diversity-generating retroelements (DGRs) create unparalleled levels of protein sequence variation through mutagenic retrohoming. Sequence information is transferred from an invariant template region (TR), through an RNA intermediate, to a protein-coding variable region. Selective infidelity at adenines during transfer is a hallmark of DGRs from disparate bacteria, archaea, and microbial viruses. We recapitulated selective infidelity in vitro for the prototypical Bordetella bacteriophage DGR. A complex of the DGR reverse transcriptase bRT and pentameric accessory variability determinant (Avd) protein along with DGR RNA were necessary and sufficient for synthesis of template-primed, covalently linked RNA–cDNA molecules, as observed in vivo. We identified RNA–cDNA molecules to be branched and most plausibly linked through 2′-5′ phosphodiester bonds. Adenine-mutagenesis was intrinsic to the bRT-Avd complex, which displayed unprecedented promiscuity while reverse transcribing adenines of either DGR or non-DGR RNA templates. In contrast, bRT-Avd processivity was strictly dependent on the template, occurring only for the DGR RNA. This restriction was mainly due to a noncoding segment downstream of TR, which specifically bound Avd and created a privileged site for processive polymerization. Restriction to DGR RNA may protect the host genome from damage. These results define the early steps in a novel pathway for massive sequence diversification.
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Affiliation(s)
- Sumit Handa
- Department of Chemistry & Biochemistry, University of California, San Diego, CA 92093, USA
| | - Yong Jiang
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sijia Tao
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Robert Foreman
- Department of Chemistry & Biochemistry, University of California, San Diego, CA 92093, USA
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jeff F Miller
- Departments of Microbiology, Immunology, and Molecular Genetics, Molecular Biology Institute, and California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Partho Ghosh
- Department of Chemistry & Biochemistry, University of California, San Diego, CA 92093, USA
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35
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Yan F, Yu X, Duan Z, Lu J, Jia B, Qiao Y, Sun C, Wei C. Discovery and characterization of the evolution, variation and functions of diversity-generating retroelements using thousands of genomes and metagenomes. BMC Genomics 2019; 20:595. [PMID: 31324156 PMCID: PMC6642488 DOI: 10.1186/s12864-019-5951-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 07/02/2019] [Indexed: 12/31/2022] Open
Abstract
Background Diversity-generating retroelements (DGRs) are a unique family of retroelements that generate sequence diversity of DNA to benefit their hosts by introducing variations and accelerating the evolution of target proteins. They exist widely in bacteria, archaea, phage and plasmid. However, our understanding about DGRs in natural environments was still very limited. Results We developed an efficient computational algorithm to identify DGRs, and applied it to characterize DGRs in more than 80,000 sequenced bacterial genomes as well as more than 4,000 human metagenome datasets. In total, we identified 948 non-redundant DGRs, which expanded the number of known DGRs in bacterial genomes and human microbiomes by about 55%, and provided a much more comprehensive reference for the study of DGRs. Phylogenetic analysis was done for identified DGRs. The putative target genes of DGRs were searched, and the functions of these target genes were investigated with a comprehensive alignment against the nr database. Conclusions DGR system is a powerful and universal mechanism to generate diversity. DGR evolution is closely associated with the living environment and their cassette structures. Furthermore, it may impact a wide range of functional processes in addition to receptor-binding. These results significantly improved our understanding about DGRs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5951-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fazhe Yan
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xuelin Yu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Zhongqu Duan
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jinyuan Lu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Ben Jia
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.,Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai, 201203, China
| | - Yuyang Qiao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Chen Sun
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Chaochun Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China. .,Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai, 201203, China.
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36
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Lannes R, Olsson-Francis K, Lopez P, Bapteste E. Carbon Fixation by Marine Ultrasmall Prokaryotes. Genome Biol Evol 2019; 11:1166-1177. [PMID: 30903144 PMCID: PMC6475129 DOI: 10.1093/gbe/evz050] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2019] [Indexed: 12/12/2022] Open
Abstract
Autotrophic carbon fixation is a crucial process for sustaining life on Earth. To date, six pathways, the Calvin–Benson–Bassham cycle, the reductive tricarboxylic acid cycle, the 3-hydroxypropionate bi-cycle, the Wood–Ljungdahl pathway, the dicarboxylate/4-hydroxybutyrate cycle, and the 4-hydroxybutyrate cycle, have been described. Nano-organisms such as members of the Candidate Phyla Radiation (CPR) bacterial superphylum and the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohalorchaeota (DPANN) archaeal superphylum could deeply impact carbon cycling and carbon fixation in ways that are still to be determined. CPR and DPANN are ubiquitous in the environment but understudied; their gene contents are not exhaustively described; and their metabolisms are not yet fully understood. Here, the completeness of each of the above pathways was quantified and tested for the presence of all key enzymes in nano-organisms from across the World Ocean. The novel marine ultrasmall prokaryotes were demonstrated to collectively harbor the genes required for carbon fixation, in particular the “energetically efficient” dicarboxylate/4-hydroxybutyrate pathway and the 4-hydroxybutyrate pathway. This contrasted with the known carbon metabolic pathways associated with CPR members in aquifers, where they are described as degraders (Castelle CJ, et al. 2015. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol. 25(6):690–701; Castelle CJ, et al. 2018. Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nat Rev Microbiol. 16(10):629–645; Anantharaman K, et al. 2016. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun. 7:13219.). Our findings suggest that nano-organisms have a broader contribution to carbon fixation and cycling than currently assumed. Furthermore, CPR and DPANN superphyla are possibly not the only nanosized prokaryotes; therefore, the discovery of new autotrophic marine nano-organisms by future single cell genomics is anticipated.
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Affiliation(s)
- Romain Lannes
- Sorbonne Université, Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Karen Olsson-Francis
- School of Environment, Earth and Ecosystems, The Open University, Milton Keynes, United Kingdom
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
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Wu L, Gingery M, Abebe M, Arambula D, Czornyj E, Handa S, Khan H, Liu M, Pohlschroder M, Shaw KL, Du A, Guo H, Ghosh P, Miller JF, Zimmerly S. Diversity-generating retroelements: natural variation, classification and evolution inferred from a large-scale genomic survey. Nucleic Acids Res 2019; 46:11-24. [PMID: 29186518 PMCID: PMC5758913 DOI: 10.1093/nar/gkx1150] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 11/04/2017] [Indexed: 01/12/2023] Open
Abstract
Diversity-generating retroelements (DGRs) are novel genetic elements that use reverse transcription to generate vast numbers of sequence variants in specific target genes. Here, we present a detailed comparative bioinformatic analysis that depicts the landscape of DGR sequences in nature as represented by data in GenBank. Over 350 unique DGRs are identified, which together form a curated reference set of putatively functional DGRs. We classify target genes, variable repeats and DGR cassette architectures, and identify two new accessory genes. The great variability of target genes implies roles of DGRs in many undiscovered biological processes. There is much evidence for horizontal transfers of DGRs, and we identify lineages of DGRs that appear to have specialized properties. Because GenBank contains data from only 10% of described species, the compilation may not be wholly representative of DGRs present in nature. Indeed, many DGR subtypes are present only once in the set and DGRs of the candidate phylum radiation bacteria, and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea archaea, are exceptionally diverse in sequence, with little information available about functions of their target genes. Nonetheless, this study provides a detailed framework for classifying and studying DGRs as they are uncovered and studied in the future.
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Affiliation(s)
- Li Wu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Mari Gingery
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael Abebe
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Diego Arambula
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Elizabeth Czornyj
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sumit Handa
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Hamza Khan
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Minghsun Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Kharissa L Shaw
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Amy Du
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Huatao Guo
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212, USA
| | - Partho Ghosh
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Jeff F Miller
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Steven Zimmerly
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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Sharifi F, Ye Y. MyDGR: a server for identification and characterization of diversity-generating retroelements. Nucleic Acids Res 2019; 47:W289-W294. [PMID: 31049585 PMCID: PMC6602519 DOI: 10.1093/nar/gkz329] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/05/2019] [Accepted: 04/23/2019] [Indexed: 01/18/2023] Open
Abstract
MyDGR is a web server providing integrated prediction and visualization of Diversity-Generating Retroelements (DGR) systems in query nucleotide sequences. It is built upon an enhanced version of DGRscan, a tool we previously developed for identification of DGR systems. DGR systems are remarkable genetic elements that use error-prone reverse transcriptases to generate vast sequence variants in specific target genes, which have been shown to benefit their hosts (bacteria, archaea or phages). As the first web server for annotation of DGR systems, myDGR is freely available on the web at http://omics.informatics.indiana.edu/myDGR with all major browsers supported. MyDGR accepts query nucleotide sequences in FASTA format, and outputs all the important features of a predicted DGR system, including a reverse transcriptase, a template repeat and one (or more) variable repeats and their alignment featuring A-to-N (N can be C, T or G) substitutions, and VR-containing target gene(s). In addition to providing the results as text files for download, myDGR generates a visual summary of the results for users to explore the predicted DGR systems. Users can also directly access pre-calculated, putative DGR systems identified in currently available reference bacterial genomes and a few other collections of sequences (including human microbiomes).
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Affiliation(s)
- Fatemeh Sharifi
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47405, USA
| | - Yuzhen Ye
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47405, USA
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García-López R, Pérez-Brocal V, Moya A. Beyond cells - The virome in the human holobiont. MICROBIAL CELL (GRAZ, AUSTRIA) 2019; 6:373-396. [PMID: 31528630 PMCID: PMC6717880 DOI: 10.15698/mic2019.09.689] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/14/2019] [Accepted: 04/03/2019] [Indexed: 01/01/2023]
Abstract
Viromics, or viral metagenomics, is a relatively new and burgeoning field of research that studies the complete collection of viruses forming part of the microbiota in any given niche. It has strong foundations rooted in over a century of discoveries in the field of virology and recent advances in molecular biology and sequencing technologies. Historically, most studies have deconstructed the concept of viruses into a simplified perception of viral agents as mere pathogens, which demerits the scope of large-scale viromic analyses. Viruses are, in fact, much more than regular parasites. They are by far the most dynamic and abundant entity and the greatest killers on the planet, as well as the most effective geo-transforming genetic engineers and resource recyclers, acting on all life strata in any habitat. Yet, most of this uncanny viral world remains vastly unexplored to date, greatly hindered by the bewildering complexity inherent to such studies and the methodological and conceptual limitations. Viromic studies are just starting to address some of these issues but they still lag behind microbial metagenomics. In recent years, however, higher-throughput analysis and resequencing have rekindled interest in a field that is just starting to show its true potential. In this review, we take a look at the scientific and technological developments that led to the advent of viral and bacterial metagenomics with a particular, but not exclusive, focus on human viromics from an ecological perspective. We also address some of the most relevant challenges that current viral studies face and ponder on the future directions of the field.
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Affiliation(s)
- Rodrigo García-López
- Institute of Evolutionary Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), València, Spain
| | - Vicente Pérez-Brocal
- Institute of Evolutionary Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), València, Spain
| | - Andrés Moya
- Institute of Evolutionary Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), València, Spain
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Abstract
We demonstrate that Candidatus Nanohaloarchaeum antarcticus requires Halorubrum lacusprofundi for growth, illustrating that Nanohaloarchaeota require a host rather than being free living as previously proposed. Developing the means of cultivating Nanohaloarchaeota in the laboratory provides the capacity to advance understanding of how archaea interact and the factors that control their symbiotic relationship (e.g. mutualism, commensalism, antagonism). Our findings amplify the view that Antarctic lakes are a treasure trove for the discovery of microbes with previously unknown properties. In hypersaline environments, Nanohaloarchaeota (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaeota [DPANN] superphylum) are thought to be free-living microorganisms. We report cultivation of 2 strains of Antarctic Nanohaloarchaeota and show that they require the haloarchaeon Halorubrum lacusprofundi for growth. By performing growth using enrichments and fluorescence-activated cell sorting, we demonstrated successful cultivation of Candidatus Nanohaloarchaeum antarcticus, purification of Ca. Nha. antarcticus away from other species, and growth and verification of Ca. Nha. antarcticus with Hrr. lacusprofundi; these findings are analogous to those required for fulfilling Koch’s postulates. We use fluorescent in situ hybridization and transmission electron microscopy to assess cell structures and interactions; metagenomics to characterize enrichment taxa, generate metagenome assembled genomes, and interrogate Antarctic communities; and proteomics to assess metabolic pathways and speculate about the roles of certain proteins. Metagenome analysis indicates the presence of a single species, which is endemic to Antarctic hypersaline systems that support the growth of haloarchaea. The presence of unusually large proteins predicted to function in attachment and invasion of hosts plus the absence of key biosynthetic pathways (e.g., lipids) in metagenome assembled genomes of globally distributed Nanohaloarchaeota indicate that all members of the lineage have evolved as symbionts. Our work expands the range of archaeal symbiotic lifestyles and provides a genetically tractable model system for advancing understanding of the factors controlling microbial symbiotic relationships.
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Abstract
The combination of modern biotechnologies such as DNA synthesis, λ red recombineering, CRISPR-based editing and next-generation high-throughput sequencing increasingly enables precise manipulation of genes and genomes. Beyond rational design, these technologies also enable the targeted, and potentially continuous, introduction of multiple mutations. While this might seem to be merely a return to natural selection, the ability to target evolution greatly reduces fitness burdens and focuses mutation and selection on those genes and traits that best contribute to a desired phenotype, ultimately throwing evolution into fast forward.
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When We Stop Thinking about Microbes as Cells. J Mol Biol 2019; 431:2487-2492. [DOI: 10.1016/j.jmb.2019.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 04/19/2019] [Accepted: 05/04/2019] [Indexed: 12/21/2022]
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Handa S, Shaw KL, Ghosh P. Crystal structure of a Thermus aquaticus diversity-generating retroelement variable protein. PLoS One 2019; 14:e0205618. [PMID: 30629599 PMCID: PMC6328139 DOI: 10.1371/journal.pone.0205618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/21/2018] [Indexed: 01/01/2023] Open
Abstract
Diversity-generating retroelements (DGRs) are widely distributed in bacteria, archaea, and microbial viruses, and bring about unparalleled levels of sequence variation in target proteins. While DGR variable proteins share low sequence identity, the structures of several such proteins have revealed the C-type lectin (CLec)-fold as a conserved scaffold for accommodating massive sequence variation. This conservation has led to the suggestion that the CLec-fold may be useful in molecular surface display applications. Thermostability is an attractive feature in such applications, and thus we studied the variable protein of a DGR encoded by a prophage of the thermophile Thermus aquaticus. We report here the 2.8 Å resolution crystal structure of the variable protein from the T. aquaticus DGR, called TaqVP, and confirm that it has a CLec-fold. Remarkably, its variable region is nearly identical in structure to those of several other CLec-fold DGR variable proteins despite low sequence identity among these. TaqVP was found to be thermostable, which appears to be a property shared by several CLec-fold DGR variable proteins. These results provide impetus for the pursuit of the DGR variable protein CLec-fold in molecular display applications.
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Affiliation(s)
- Sumit Handa
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, United States of America
| | - Kharissa L. Shaw
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, United States of America
| | - Partho Ghosh
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, United States of America
- * E-mail:
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Dombrowski N, Lee JH, Williams TA, Offre P, Spang A. Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. FEMS Microbiol Lett 2019; 366:5281434. [PMID: 30629179 PMCID: PMC6349945 DOI: 10.1093/femsle/fnz008] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/07/2019] [Indexed: 12/16/2022] Open
Abstract
Archaea-a primary domain of life besides Bacteria-have for a long time been regarded as peculiar organisms that play marginal roles in biogeochemical cycles. However, this picture changed with the discovery of a large diversity of archaea in non-extreme environments enabled by the use of cultivation-independent methods. These approaches have allowed the reconstruction of genomes of uncultivated microorganisms and revealed that archaea are diverse and broadly distributed in the biosphere and seemingly include a large diversity of putative symbiotic organisms, most of which belong to the tentative archaeal superphylum referred to as DPANN. This archaeal group encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, many members of DPANN may be obligately dependent on symbiotic interactions with other organisms and may even include novel parasites. In this contribution, we review the current knowledge of the gene repertoires and lifestyles of members of this group and discuss their placement in the tree of life, which is the basis for our understanding of the deep microbial roots and the role of symbiosis in the evolution of life on Earth.
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Affiliation(s)
- Nina Dombrowski
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA
| | - Jun-Hoe Lee
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, P.O. Box 596, Husargatan 3, SE-75123 Uppsala, Sweden
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol, Bristol BS8 1TQ, UK
| | - Pierre Offre
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
| | - Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, P.O. Box 596, Husargatan 3, SE-75123 Uppsala, Sweden
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Genome size evolution in the Archaea. Emerg Top Life Sci 2018; 2:595-605. [PMID: 33525826 PMCID: PMC7289037 DOI: 10.1042/etls20180021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/26/2018] [Accepted: 09/28/2018] [Indexed: 11/17/2022]
Abstract
What determines variation in genome size, gene content and genetic diversity at the broadest scales across the tree of life? Much of the existing work contrasts eukaryotes with prokaryotes, the latter represented mainly by Bacteria. But any general theory of genome evolution must also account for the Archaea, a diverse and ecologically important group of prokaryotes that represent one of the primary domains of cellular life. Here, we survey the extant diversity of Bacteria and Archaea, and ask whether the general principles of genome evolution deduced from the study of Bacteria and eukaryotes also apply to the archaeal domain. Although Bacteria and Archaea share a common prokaryotic genome architecture, the extant diversity of Bacteria appears to be much higher than that of Archaea. Compared with Archaea, Bacteria also show much greater genome-level specialisation to specific ecological niches, including parasitism and endosymbiosis. The reasons for these differences in long-term diversification rates are unclear, but might be related to fundamental differences in informational processing machineries and cell biological features that may favour archaeal diversification in harsher or more energy-limited environments. Finally, phylogenomic analyses suggest that the first Archaea were anaerobic autotrophs that evolved on the early Earth.
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Benler S, Cobián-Güemes AG, McNair K, Hung SH, Levi K, Edwards R, Rohwer F. A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage. MICROBIOME 2018; 6:191. [PMID: 30352623 PMCID: PMC6199706 DOI: 10.1186/s40168-018-0573-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/08/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Diversity-generating retroelements (DGRs) are genetic cassettes that selectively mutate target genes to produce hypervariable proteins. First characterized in Bordetella bacteriophage BPP-1, the DGR creates a hypervariable phage tail fiber that enables host tropism switching. Subsequent surveys for DGRs conclude that the majority identified to date are bacterial or archaeal in origin. This work examines bacteriophage and bacterial genomes for novel phage-encoded DGRs. RESULTS This survey discovered 92 DGRs that were only found in phages exhibiting a temperate lifestyle. The majority of phage-encoded DGRs were identified as prophages in bacterial hosts from the phyla Bacteroidetes, Proteobacteria, and Firmicutes. Sequence reads from these previously unidentified prophages were present in viral metagenomes (viromes), indicating these prophages can produce functional viruses. Five phages possessed hypervariable proteins with structural similarity to the tail fiber of BPP-1, whereas the functions of the remaining DGR target proteins were unknown. A novel temperate phage that harbors a DGR cassette targeting a protein of unknown function was induced from Bacteroides dorei. This phage, here named Bacteroides dorei Hankyphage, lysogenizes 13 different Bacteroides species and was present in 34% and 21% of whole-community metagenomes and human-associated viromes, respectively. CONCLUSIONS Here, the number of known DGR-containing phages is increased from four to 92. All of these phages exhibit a temperate lifestyle, including a cosmopolitan human-associated phage. Targeted hypervariation by temperate phages may be a ubiquitous mechanism underlying phage-bacteria interaction in the human microbiome.
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Affiliation(s)
- Sean Benler
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
| | | | - Katelyn McNair
- Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
| | - Shr-Hau Hung
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
| | - Rob Edwards
- Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
| | - Forest Rohwer
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182 USA
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Bernard G, Pathmanathan JS, Lannes R, Lopez P, Bapteste E. Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery. Genome Biol Evol 2018; 10:707-715. [PMID: 29420719 PMCID: PMC5830969 DOI: 10.1093/gbe/evy031] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2018] [Indexed: 02/07/2023] Open
Abstract
Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns.
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Affiliation(s)
- Guillaume Bernard
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), France
| | - Jananan S Pathmanathan
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), France
| | - Romain Lannes
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), France
| | - Philippe Lopez
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), France
| | - Eric Bapteste
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), France
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Jarett JK, Nayfach S, Podar M, Inskeep W, Ivanova NN, Munson-McGee J, Schulz F, Young M, Jay ZJ, Beam JP, Kyrpides NC, Malmstrom RR, Stepanauskas R, Woyke T. Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis. MICROBIOME 2018; 6:161. [PMID: 30223889 PMCID: PMC6142677 DOI: 10.1186/s40168-018-0539-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 08/26/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Nanoarchaeota are obligate symbionts of other Archaea first discovered 16 years ago, yet little is known about this largely uncultivated taxon. While Nanoarchaeota diversity has been detected in a variety of habitats using 16S rRNA gene surveys, genome sequences have been available for only three Nanoarchaeota and their hosts. The host range and adaptation of Nanoarchaeota to a wide range of environmental conditions has thus largely remained elusive. Single-cell genomics is an ideal approach to address these questions as Nanoarchaeota can be isolated while still attached to putative hosts, enabling the exploration of cell-cell interactions and fine-scale genomic diversity. RESULTS From 22 single amplified genomes (SAGs) from three hot springs in Yellowstone National Park, we derived a genome-based phylogeny of the phylum Nanoarchaeota, linking it to global 16S rRNA gene diversity. By exploiting sequencing of co-sorted tightly attached cells, we associated Nanoarchaeota with 6 novel putative hosts, 2 of which were found in multiple SAGs, and showed that the same host species may associate with multiple species of Nanoarchaeota. Comparison of single nucleotide polymorphisms (SNPs) within a population of Nanoarchaeota SAGs indicated that Nanoarchaeota attached to a single host cell in situ are likely clonal. In addition to an overall pattern of purifying selection, we found significantly higher densities of non-synonymous SNPs in hypothetical cell surface proteins, as compared to other functional categories. Genes implicated in interactions in other obligate microbe-microbe symbioses, including those encoding a cytochrome bd-I ubiquinol oxidase and a FlaJ/TadC homologue possibly involved in type IV pili production, also had relatively high densities of non-synonymous SNPs. CONCLUSIONS This population genetics study of Nanoarchaeota greatly expands the known potential host range of the phylum and hints at what genes may be involved in adaptation to diverse environments or different hosts. We provide the first evidence that Nanoarchaeota cells attached to the same host cell are clonal and propose a hypothesis for how clonality may occur despite diverse symbiont populations.
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Affiliation(s)
| | | | - Mircea Podar
- Oak Ridge National Laboratory, Oak Ridge, TN USA
- Department of Microbiology, University of Tennessee, Knoxville, TN USA
| | - William Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT USA
| | | | - Jacob Munson-McGee
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT USA
| | | | - Mark Young
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT USA
| | - Zackary J. Jay
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT USA
| | - Jacob P. Beam
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT USA
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME USA
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
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Liu X, Li M, Castelle CJ, Probst AJ, Zhou Z, Pan J, Liu Y, Banfield JF, Gu JD. Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages. MICROBIOME 2018; 6:102. [PMID: 29884244 PMCID: PMC5994134 DOI: 10.1186/s40168-018-0488-2] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/25/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND As a recently discovered member of the DPANN superphylum, Woesearchaeota account for a wide diversity of 16S rRNA gene sequences, but their ecology, evolution, and metabolism remain largely unknown. RESULTS Here, we assembled 133 global clone libraries/studies and 19 publicly available genomes to profile these patterns for Woesearchaeota. Phylogenetic analysis shows a high diversity with 26 proposed subgroups for this recently discovered archaeal phylum, which are widely distributed in different biotopes but primarily in inland anoxic environments. Ecological patterns analysis and ancestor state reconstruction for specific subgroups reveal that oxic status of the environments is the key factor driving the distribution and evolutionary diversity of Woesearchaeota. A selective distribution to different biotopes and an adaptive colonization from anoxic to oxic environments can be proposed and supported by evidence of the presence of ferredoxin-dependent pathways in the genomes only from anoxic biotopes but not from oxic biotopes. Metabolic reconstructions support an anaerobic heterotrophic lifestyle with conspicuous metabolic deficiencies, suggesting the requirement for metabolic complementarity with other microbes. Both lineage abundance distribution and co-occurrence network analyses across diverse biotopes confirmed metabolic complementation and revealed a potential syntrophic relationship between Woesearchaeota and methanogens, which is supported by metabolic modeling. If correct, Woesearchaeota may impact methanogenesis in inland ecosystems. CONCLUSIONS The findings provide an ecological and evolutionary framework for Woesearchaeota at a global scale and indicate their potential ecological roles, especially in methanogenesis.
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Affiliation(s)
- Xiaobo Liu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518000, China.
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, 336 Hilgard Hall, Berkeley, CA, 94720, USA
| | - Alexander J Probst
- Department of Earth and Planetary Science, University of California, Berkeley, 336 Hilgard Hall, Berkeley, CA, 94720, USA
- Group for Aquatic Microbial Ecology (GAME), Biofilm Center, Department of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
| | - Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518000, China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518000, China
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, 336 Hilgard Hall, Berkeley, CA, 94720, USA
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China.
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, 999077, China.
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Core Concepts: How diversity-generating retroelements promote mutation and adaptation in myriad microbes. Proc Natl Acad Sci U S A 2018; 114:10509-10511. [PMID: 29073036 DOI: 10.1073/pnas.1714687114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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