1
|
Roughgarden J. Lytic/Lysogenic Transition as a Life-History Switch. Virus Evol 2024; 10:veae028. [PMID: 38756985 PMCID: PMC11097211 DOI: 10.1093/ve/veae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/15/2024] [Accepted: 03/27/2024] [Indexed: 05/18/2024] Open
Abstract
The transition between lytic and lysogenic life cycles is the most important feature of the life-history of temperate viruses. To explain this transition, an optimal life-history model is offered based a discrete-time formulation of phage/bacteria population dynamics that features infection of bacteria by Poisson sampling of virions from the environment. The time step is the viral latency period. In this model, density-dependent viral absorption onto the bacterial surface produces virus/bacteria coexistence and density dependence in bacterial growth is not needed. The formula for the transition between lytic and lysogenic phases is termed the 'fitness switch'. According to the model, the virus switches from lytic to lysogenic when its population grows faster as prophage than as virions produced by lysis of the infected cells, and conversely for the switch from lysogenic to lytic. A prophage that benefits the bacterium it infects automatically incurs lower fitness upon exiting the bacterial genome, resulting in its becoming locked into the bacterial genome in what is termed here as a 'prophage lock'. The fitness switch qualitatively predicts the ecogeographic rule that environmental enrichment leads to microbialization with a concomitant increase in lysogeny, fluctuating environmental conditions promote virus-mediated horizontal gene transfer, and prophage-containing bacteria can integrate into the microbiome of a eukaryotic host forming a functionally integrated tripartite holobiont. These predictions accord more with the 'Piggyback-the-Winner' hypothesis than with the 'Kill-the-Winner' hypothesis in virus ecology.
Collapse
Affiliation(s)
- Joan Roughgarden
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, HI 96744, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
2
|
Ji Y, Xi H, Chen C, Sun C, Feng X, Lei L, Han W, Gu J. The pig intestinal phageome is an important reservoir and transfer vector for virulence genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170076. [PMID: 38220020 DOI: 10.1016/j.scitotenv.2024.170076] [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: 11/06/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
Bacteriophages (phages) can significantly influence the composition and functions of their host communities, and enhance host pathogenicity via the transport of phage-encoded virulence genes. Phages are the main component of animal gut viruses, however, there are few reports on the piglet gut phageome and its contribution to virulence genes. Here, a total of 185 virulence genes from 59,955 predicted genes of gut phages in weaned piglets were identified, with 0.688 % of the phage contigs coding for at least one virulence gene. The virulence gene pblA was the most abundant, with various virulence genes significantly correlated with gut phages and their encoded mobile gene element (MGE) genes. Importantly, multiple virulence genes and MGE genes coexist in some phage sequences, and up to 12 virulence genes were detected in a single phage sequence, greatly increasing the risk of phage-mediated transmission of virulence genes into the bacterial genome. In addition, diarrhoea has driven changes in the composition and structure of phage and bacterial communities in the intestinal tract of weaned piglets, significantly increasing the abundance of phage contigs encoding both virulence genes and MGE genes in faecal samples, which potentially increases the risk of phage-mediated virulence genes being transfected into the gut bacterial genome. In summary, this study expands our understanding of the gut microbiome of piglets, advances our understanding of the potential role of phages in driving host pathogenesis in the gut system, and provides new insights into the sources of virulence genes and genetic evolution of bacteria in pig farm environments.
Collapse
Affiliation(s)
- Yalu Ji
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Hengyu Xi
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Chong Chen
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Changjiang Sun
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xin Feng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Liancheng Lei
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Wenyu Han
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jingmin Gu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun 130062, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
| |
Collapse
|
3
|
Voolstra CR, Raina JB, Dörr M, Cárdenas A, Pogoreutz C, Silveira CB, Mohamed AR, Bourne DG, Luo H, Amin SA, Peixoto RS. The coral microbiome in sickness, in health and in a changing world. Nat Rev Microbiol 2024:10.1038/s41579-024-01015-3. [PMID: 38438489 DOI: 10.1038/s41579-024-01015-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 03/06/2024]
Abstract
Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthropogenic environmental change. Corals are holobionts that comprise the cnidarian animal host and a diverse community of bacteria, archaea, viruses and eukaryotic microorganisms. Recent research shows that the bacterial microbiome has a pivotal role in coral biology. A healthy bacterial assemblage contributes to nutrient cycling and stress resilience, but pollution, overfishing and climate change can break down these symbiotic relationships, which results in disease, bleaching and, ultimately, coral death. Although progress has been made in characterizing the spatial-temporal diversity of bacteria, we are only beginning to appreciate their functional contribution. In this Review, we summarize the ecological and metabolic interactions between bacteria and other holobiont members, highlight the biotic and abiotic factors influencing the structure of bacterial communities and discuss the impact of climate change on these communities and their coral hosts. We emphasize how microbiome-based interventions can help to decipher key mechanisms underpinning coral health and promote reef resilience. Finally, we explore how recent technological developments may be harnessed to address some of the most pressing challenges in coral microbiology, providing a road map for future research in this field.
Collapse
Affiliation(s)
| | - Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales, Australia.
| | - Melanie Dörr
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Anny Cárdenas
- Department of Biology, American University, Washington, DC, USA
| | - Claudia Pogoreutz
- PSL Université Paris: EPHE-UPVD-CNRS, UAR 3278 CRIOBE, Université de Perpignan, Perpignan, France
| | | | - Amin R Mohamed
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Haiwei Luo
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, State Key Laboratory of Agrobiotechnology and Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shady A Amin
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Raquel S Peixoto
- Red Sea Research Center (RSRC) and Computational Biology Research Center (CBRC), Biological, Environmental Sciences, and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| |
Collapse
|
4
|
Zhou K, Zhang T, Chen XW, Xu Y, Zhang R, Qian PY. Viruses in Marine Invertebrate Holobionts: Complex Interactions Between Phages and Bacterial Symbionts. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:467-485. [PMID: 37647612 DOI: 10.1146/annurev-marine-021623-093133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Marine invertebrates are ecologically and economically important and have formed holobionts by evolving symbiotic relationships with cellular and acellular microorganisms that reside in and on their tissues. In recent decades, significant focus on symbiotic cellular microorganisms has led to the discovery of various functions and a considerable expansion of our knowledge of holobiont functions. Despite this progress, our understanding of symbiotic acellular microorganisms remains insufficient, impeding our ability to achieve a comprehensive understanding of marine holobionts. In this review, we highlight the abundant viruses, with a particular emphasis on bacteriophages; provide an overview of their diversity, especially in extensively studied sponges and corals; and examine their potential life cycles. In addition, we discuss potential phage-holobiont interactions of various invertebrates, including participating in initial bacterial colonization, maintaining symbiotic relationships, and causing or exacerbating the diseases of marine invertebrates. Despite the importance of this subject, knowledge of how viruses contribute to marine invertebrate organisms remains limited. Advancements in technology and greater attention to viruses will enhance our understanding of marine invertebrate holobionts.
Collapse
Affiliation(s)
- Kun Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China;
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Ting Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Xiao-Wei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China;
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China;
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China;
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| |
Collapse
|
5
|
Rossi FPN, Flores VS, Uceda-Campos G, Amgarten DE, Setubal JC, da Silva AM. Comparative Analyses of Bacteriophage Genomes. Methods Mol Biol 2024; 2802:427-453. [PMID: 38819567 DOI: 10.1007/978-1-0716-3838-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Bacterial viruses (bacteriophages or phages) are the most abundant and diverse biological entities on Earth. There is a renewed worldwide interest in phage-centered research motivated by their enormous potential as antimicrobials to cope with multidrug-resistant pathogens. An ever-growing number of complete phage genomes are becoming available, derived either from newly isolated phages (cultivated phages) or recovered from metagenomic sequencing data (uncultivated phages). Robust comparative analysis is crucial for a comprehensive understanding of genotypic variations of phages and their related evolutionary processes, and to investigate the interaction mechanisms between phages and their hosts. In this chapter, we present a protocol for phage comparative genomics employing tools selected out of the many currently available, focusing on complete genomes of phages classified in the class Caudoviricetes. This protocol provides accurate identification of similarities, differences, and patterns among new and previously known complete phage genomes as well as phage clustering and taxonomic classification.
Collapse
Affiliation(s)
| | - Vinicius Sousa Flores
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | - Guillermo Uceda-Campos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | | | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil.
| |
Collapse
|
6
|
Liu Y, Jiao N, Xu Zhong K, Zang L, Zhang R, Xiao X, Shi Y, Zhang Z, Tao Y, Bai L, Gao B, Yang Y, Huang X, Ji M, Liu J, Liu P, Yao T. Diversity and function of mountain and polar supraglacial DNA viruses. Sci Bull (Beijing) 2023; 68:2418-2433. [PMID: 37739838 DOI: 10.1016/j.scib.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/29/2023] [Accepted: 06/30/2023] [Indexed: 09/24/2023]
Abstract
Mountain and polar glaciers cover 10% of the Earth's surface and are typically extreme environments that challenge life of all forms. Viruses are abundant and active in supraglacial ecosystems and play a crucial role in controlling the supraglacial microbial communities. However, our understanding of virus ecology on glacier surfaces and their potential impacts on downstream ecosystems remains limited. Here, we present the supraglacial virus genome (SgVG) catalog, a 15-fold expanded genomic inventory of 10,840 DNA-virus species from 38 mountain and polar glaciers, spanning habitats such as snow, ice, meltwater, and cryoconite. Supraglacial DNA-viruses were highly specific compared to viruses in other ecosystems yet exhibited low public health risks. Supraglacial viral communities were primarily constrained by habitat, with cryoconite displaying the highest viral activity levels. We observed a prevalence of lytic viruses in all habitats, especially in cryoconite, but a high level of lysogenic viruses in snow and ice. Additionally, we found that supraglacial viruses could be linked to ∼83% of obtained prokaryotic phyla/classes and possessed the genetic potential to promote metabolism and increase cold adaptation, cell mobility, and phenolic carbon use of hosts in hostile environmental conditions using diverse auxiliary metabolic genes. Our results provide the first systematic characterization of the diversity, function, and public health risks evaluation of mountain and polar supraglacial DNA viruses. This understanding of glacial viruses is crucial for function assessments and ecological modeling of glacier ecosystems, especially for the Tibetan Plateau's Mountain glaciers, which support ∼20% of the human populations on Earth.
Collapse
Affiliation(s)
- Yongqin Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China; State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China.
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Kevin Xu Zhong
- Department of Earth, Ocean, and Atmospheric Sciences, The University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Lin Zang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen 518000, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi Shi
- University of Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihao Zhang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China
| | - Ye Tao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Liping Bai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, China
| | - Bianli Gao
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Xingyu Huang
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Mukan Ji
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Junzhi Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Pengfei Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China.
| | - Tandong Yao
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| |
Collapse
|
7
|
Silveira CB, Luque A, Haas AF, Roach TNF, George EE, Knowles B, Little M, Sullivan CJ, Varona NS, Wegley Kelly L, Brainard R, Rohwer F, Bailey B. Viral predation pressure on coral reefs. BMC Biol 2023; 21:77. [PMID: 37038111 PMCID: PMC10088212 DOI: 10.1186/s12915-023-01571-9] [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: 06/23/2022] [Accepted: 03/17/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Predation pressure and herbivory exert cascading effects on coral reef health and stability. However, the extent of these cascading effects can vary considerably across space and time. This variability is likely a result of the complex interactions between coral reefs' biotic and abiotic dimensions. A major biological component that has been poorly integrated into the reefs' trophic studies is the microbial community, despite its role in coral death and bleaching susceptibility. Viruses that infect bacteria can control microbial densities and may positively affect coral health by controlling microbialization. We hypothesize that viral predation of bacteria has analogous effects to the top-down pressure of macroorganisms on the trophic structure and reef health. RESULTS Here, we investigated the relationships between live coral cover and viruses, bacteria, benthic algae, fish biomass, and water chemistry in 110 reefs spanning inhabited and uninhabited islands and atolls across the Pacific Ocean. Statistical learning showed that the abundance of turf algae, viruses, and bacteria, in that order, were the variables best predicting the variance in coral cover. While fish biomass was not a strong predictor of coral cover, the relationship between fish and corals became apparent when analyzed in the context of viral predation: high coral cover (> 50%) occurred on reefs with a combination of high predator fish biomass (sum of sharks and piscivores > 200 g m-2) and high virus-to-bacteria ratios (> 10), an indicator of viral predation pressure. However, these relationships were non-linear, with reefs at the higher and lower ends of the coral cover continuum displaying a narrow combination of abiotic and biotic variables, while reefs at intermediate coral cover showed a wider range of parameter combinations. CONCLUSIONS The results presented here support the hypothesis that viral predation of bacteria is associated with high coral cover and, thus, coral health and stability. We propose that combined predation pressures from fishes and viruses control energy fluxes, inhibiting the detrimental accumulation of ecosystem energy in the microbial food web.
Collapse
Affiliation(s)
- Cynthia B Silveira
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, 33149, USA.
| | - Antoni Luque
- Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA
- Computational Science Research Center, San Diego State University, San Diego, CA, 92182, USA
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, 92182, USA
| | - Andreas F Haas
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Ty N F Roach
- Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Emma E George
- Botany Department, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ben Knowles
- Department of Ecology and Evolutionary Biology, UC Los Angeles, Los Angeles, CA, 90095, USA
| | - Mark Little
- Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | | | - Natascha S Varona
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Linda Wegley Kelly
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92037, USA
| | - Russel Brainard
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
- Pacific Islands Fisheries Science Center, National Oceanic & Atmospheric Administration, Honolulu, HI, 96818, USA
| | - Forest Rohwer
- Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Barbara Bailey
- Viral Information Institute, San Diego State University, San Diego, CA, 92182, USA.
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, 92182, USA.
| |
Collapse
|
8
|
Bi L, Han LL, Du S, Yu DT, He JZ, Zhang LM, Hu HW. Cross-biome soil viruses as an important reservoir of virulence genes. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130111. [PMID: 36209605 DOI: 10.1016/j.jhazmat.2022.130111] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/24/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Viruses can significantly influence the composition and functions of their host communities and enhance host pathogenicity via the transport of virus-encoded virulence genes. However, the contribution of viral communities to the dissemination of virulence genes across various biomes across a large scale is largely unknown. Here, we constructed 29,283 soil viral contigs (SVCs) from viral size fraction metagenomes and public databases. A total of 1310 virulence genes were identified from 1164 SVCs in a wide variety of soil biomes, including grassland, agricultural and forest soils. The virulence gene gmd was the most abundant one, followed by csrA, evpJ, and pblA. A great proportion of viruses encoding virulence genes were uncharacterized. Virus-host linkage analysis revealed that most viruses were linked to only one bacterial genus, whereas several SVCs were associated with more than one bacterial genus and even two bacterial phyla, suggesting the potential risk of spreading virulence genes across different bacterial communities via viruses. Altogether, we provided new evidence for the prevalence of virulence genes in soil viruses across biomes, which advanced our understanding of the potential role of soil viruses in driving the pathogenesis of their hosts in terrestrial ecosystems.
Collapse
Affiliation(s)
- Li Bi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Shuai Du
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan-Ting Yu
- School of Geographical Sciences, Fujian Normal University, Fujian 350007, China
| | - Ji-Zheng He
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| |
Collapse
|
9
|
Almeida A. Editorial: Insights in phage biology: 2021. Front Microbiol 2022; 13:1052366. [DOI: 10.3389/fmicb.2022.1052366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
|
10
|
Phage Diving: An Exploration of the Carcharhinid Shark Epidermal Virome. Viruses 2022; 14:v14091969. [PMID: 36146775 PMCID: PMC9500685 DOI: 10.3390/v14091969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/18/2022] Open
Abstract
The epidermal microbiome is a critical element of marine organismal immunity, but the epidermal virome of marine organisms remains largely unexplored. The epidermis of sharks represents a unique viromic ecosystem. Sharks secrete a thin layer of mucus which harbors a diverse microbiome, while their hydrodynamic dermal denticles simultaneously repel environmental microbes. Here, we sampled the virome from the epidermis of three shark species in the family Carcharhinidae: the genetically and morphologically similar Carcharhinus obscurus (n = 6) and Carcharhinus galapagensis (n = 10) and the outgroup Galeocerdo cuvier (n = 15). Virome taxonomy was characterized using shotgun metagenomics and compared with a suite of multivariate analyses. All three sharks retain species-specific but highly similar epidermal viromes dominated by uncharacterized bacteriophages which vary slightly in proportional abundance within and among shark species. Intraspecific variation was lower among C. galapagensis than among C. obscurus and G. cuvier. Using both the annotated and unannotated reads, we were able to determine that the Carcharhinus galapagensis viromes were more similar to that of G. cuvier than they were to that of C. obscurus, suggesting that behavioral niche may be a more prominent driver of virome than host phylogeny.
Collapse
|
11
|
Nawel Z, Rima O, Amira B. An overview on Vibrio temperate phages: Integration mechanisms, pathogenicity, and lysogeny regulation. Microb Pathog 2022; 165:105490. [DOI: 10.1016/j.micpath.2022.105490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 12/21/2022]
|
12
|
Bi L, Yu DT, Han LL, Du S, Yuan CY, He JZ, Hu HW. Unravelling the ecological complexity of soil viromes: Challenges and opportunities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 812:152217. [PMID: 34890674 DOI: 10.1016/j.scitotenv.2021.152217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 06/13/2023]
Abstract
Viruses are extremely abundant and ubiquitous in soil, and significantly contribute to various terrestrial ecosystem processes such as biogeochemical nutrient cycling, microbiome regulation and community assembly, and host evolutionary dynamics. Despite their numerous dominance and functional importance, understanding soil viral ecology is a formidable challenge, because of the technological challenges to characterize the abundance, diversity and community compositions of viruses, and their interactions with other organisms in the complex soil environment. Viruses may engage in a myriad of biological interactions within soil food webs across a broad range of spatiotemporal scales and are exposed to various biotic and abiotic disturbances. Current studies on the soil viromes, however, often describe the complexity of their tremendous diversity, but lack of exploring their potential ecological roles. In this article, we summarized the major methods to decipher the ecology of soil viruses, discussed biotic and abiotic factors and global change factors that shape the diversity and composition of soil viromes, and the ecological roles of soil viruses. We also proposed a new framework to understand the ecological complexity of viruses from micro to macro ecosystem scales and to predict and unravel their activities in terrestrial ecosystems.
Collapse
Affiliation(s)
- Li Bi
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Dan-Ting Yu
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, Fujian Normal University, Fujian 350007, China; School of Geographical Sciences, Fujian Normal University, Fujian 350007, China.
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shuai Du
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng-Yu Yuan
- State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, Fujian Normal University, Fujian 350007, China; School of Geographical Sciences, Fujian Normal University, Fujian 350007, China
| | - Ji-Zheng He
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| |
Collapse
|
13
|
Predicting the capsid architecture of phages from metagenomic data. Comput Struct Biotechnol J 2022; 20:721-732. [PMID: 35140890 PMCID: PMC8814770 DOI: 10.1016/j.csbj.2021.12.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 12/29/2022] Open
Abstract
Tailed phages are viruses that infect bacteria and are the most abundant biological entities on Earth. Their ecological, evolutionary, and biogeochemical roles in the planet stem from their genomic diversity. Known tailed phage genomes range from 10 to 735 kilobase pairs thanks to the size variability of the protective protein capsids that store them. However, the role of tailed phage capsids’ diversity in ecosystems is unclear. A fundamental gap is the difficulty of associating genomic information with viral capsids in the environment. To address this problem, here, we introduce a computational approach to predict the capsid architecture (T-number) of tailed phages using the sequence of a single gene—the major capsid protein. This approach relies on an allometric model that relates the genome length and capsid architecture of tailed phages. This allometric model was applied to isolated phage genomes to generate a library that associated major capsid proteins and putative capsid architectures. This library was used to train machine learning methods, and the most computationally scalable model investigated (random forest) was applied to human gut metagenomes. Compared to isolated phages, the analysis of gut data reveals a large abundance of mid-sized (T = 7) capsids, as expected, followed by a relatively large frequency of jumbo-like tailed phage capsids (T ≥ 25) and small capsids (T = 4) that have been under-sampled. We discussed how to increase the method’s accuracy and how to extend the approach to other viruses. The computational pipeline introduced here opens the doors to monitor the ongoing evolution and selection of viral capsids across ecosystems.
Collapse
|
14
|
Ramos-Barbero MD, Viver T, Zabaleta A, Senel E, Gomariz M, Antigüedad I, Santos F, Martínez-García M, Rosselló-Móra R, Antón J. Ancient saltern metagenomics: tracking changes in microbes and their viruses from the underground to the surface. Environ Microbiol 2021; 23:3477-3498. [PMID: 34110059 DOI: 10.1111/1462-2920.15630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/26/2021] [Accepted: 06/06/2021] [Indexed: 11/28/2022]
Abstract
Microbial communities in hypersaline underground waters derive from ancient organisms trapped within the evaporitic salt crystals and are part of the poorly known subterranean biosphere. Here, we characterized the viral and prokaryotic assemblages present in the hypersaline springs that dissolve Triassic-Keuper evaporite rocks and feed the Añana Salt Valley (Araba/Alava, Basque Country, Spain). Four underground water samples (around 23% total salinity) with different levels of exposure to the open air were analysed by means of microscopy and metagenomics. Cells and viruses in the spring water had lower concentrations than what are normally found in hypersaline environments and seemed to be mostly inactive. Upon exposure to the open air, there was an increase in activity of both cells and viruses as well as a selection of phylotypes. The underground water was inhabited by a rich community harbouring a diverse set of genes coding for retinal binding proteins. A total of 35 viral contigs from 15 to 104 kb, representing partial or total viral genomes, were assembled and their evolutionary changes through the spring system were followed by SNP analysis and metagenomic island tracking. Overall, both the viral and the prokaryotic assemblages changed quickly upon exposure to the open air conditions.
Collapse
Affiliation(s)
- Mª Dolores Ramos-Barbero
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (IMEDEA; CSIC-UIB), Esporles, Illes Balears, 07190, Spain
| | - Ane Zabaleta
- Hydro-Environmental Processes Group, Geology Department, Science and Technology Faculty, University of the Basque Country UPV/EHU, Leioa, 48940, Spain
| | - Ece Senel
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain.,Department of Biology, Institute of Graduate Programs, Eskisehir Technical University, Yunusemre Campus, Eskisehir, 26470, Turkey
| | - María Gomariz
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| | - Iñaki Antigüedad
- Hydro-Environmental Processes Group, Geology Department, Science and Technology Faculty, University of the Basque Country UPV/EHU, Leioa, 48940, Spain
| | - Fernando Santos
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| | - Manuel Martínez-García
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (IMEDEA; CSIC-UIB), Esporles, Illes Balears, 07190, Spain
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| |
Collapse
|
15
|
Silveira CB, Luque A, Rohwer F. The landscape of lysogeny across microbial community density, diversity and energetics. Environ Microbiol 2021; 23:4098-4111. [PMID: 34121301 DOI: 10.1111/1462-2920.15640] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 12/11/2022]
Abstract
Lysogens are common at high bacterial densities, an observation that contrasts with the prevailing view of lysogeny as a low-density refugium strategy. Here, we review the mechanisms regulating lysogeny in complex communities and show that the additive effects of coinfections, diversity and host energic status yield a bimodal distribution of lysogeny as a function of microbial densities. At high cell densities (above 106 cells ml-1 or g-1 ) and low diversity, coinfections by two or more phages are frequent and excess energy availability stimulates inefficient metabolism. Both mechanisms favour phage integration and characterize the Piggyback-the-Winner dynamic. At low densities (below 105 cells ml-1 or g-1 ), starvation represses lytic genes and extends the time window for lysogenic commitment, resulting in a higher frequency of coinfections that cause integration. This pattern follows the predictions of the refugium hypothesis. At intermediary densities (between 105 and 106 cells ml-1 or g-1 ), encounter rates and efficient energy metabolism favour lysis. This may involve Kill-the-Winner lytic dynamics and induction. Based on these three regimes, we propose a framework wherein phage integration occurs more frequently at both ends of the host density gradient, with distinct underlying molecular mechanisms (coinfections and host metabolism) dominating at each extreme.
Collapse
Affiliation(s)
- Cynthia B Silveira
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, FL, 33143, USA.,Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - Antoni Luque
- Viral Information Institute, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA.,Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA.,Computational Science Research Center, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Forest Rohwer
- Viral Information Institute, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA.,Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| |
Collapse
|
16
|
Townsend EM, Kelly L, Muscatt G, Box JD, Hargraves N, Lilley D, Jameson E. The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome. Front Cell Infect Microbiol 2021; 11:643214. [PMID: 34150671 PMCID: PMC8213399 DOI: 10.3389/fcimb.2021.643214] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/19/2021] [Indexed: 12/14/2022] Open
Abstract
The investigation of the microbial populations of the human body, known as the microbiome, has led to a revolutionary field of science, and understanding of its impacts on human development and health. The majority of microbiome research to date has focussed on bacteria and other kingdoms of life, such as fungi. Trailing behind these is the interrogation of the gut viruses, specifically the phageome. Bacteriophages, viruses that infect bacterial hosts, are known to dictate the dynamics and diversity of bacterial populations in a number of ecosystems. However, the phageome of the human gut, while of apparent importance, remains an area of many unknowns. In this paper we discuss the role of bacteriophages within the human gut microbiome. We examine the methods used to study bacteriophage populations, how this evolved over time and what we now understand about the phageome. We review the phageome development in infancy, and factors that may influence phage populations in adult life. The role and action of the phageome is then discussed at both a biological-level, and in the broader context of human health and disease.
Collapse
Affiliation(s)
- Eleanor M Townsend
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Lucy Kelly
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - George Muscatt
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Joshua D Box
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Nicole Hargraves
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Daniel Lilley
- Warwick Medical School, The University of Warwick, Coventry, United Kingdom
| | - Eleanor Jameson
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| |
Collapse
|
17
|
Forcone K, Coutinho FH, Cavalcanti GS, Silveira CB. Prophage Genomics and Ecology in the Family Rhodobacteraceae. Microorganisms 2021; 9:microorganisms9061115. [PMID: 34064105 PMCID: PMC8224337 DOI: 10.3390/microorganisms9061115] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022] Open
Abstract
Roseobacters are globally abundant bacteria with critical roles in carbon and sulfur biogeochemical cycling. Here, we identified 173 new putative prophages in 79 genomes of Rhodobacteraceae. These prophages represented 1.3 ± 0.15% of the bacterial genomes and had no to low homology with reference and metagenome-assembled viral genomes from aquatic and terrestrial ecosystems. Among the newly identified putative prophages, 35% encoded auxiliary metabolic genes (AMGs), mostly involved in secondary metabolism, amino acid metabolism, and cofactor and vitamin production. The analysis of integration sites and gene homology showed that 22 of the putative prophages were actually gene transfer agents (GTAs) similar to a GTA of Rhodobacter capsulatus. Twenty-three percent of the predicted prophages were observed in the TARA Oceans viromes generated from free viral particles, suggesting that they represent active prophages capable of induction. The distribution of these prophages was significantly associated with latitude and temperature. The prophages most abundant at high latitudes encoded acpP, an auxiliary metabolic gene involved in lipid synthesis and membrane fluidity at low temperatures. Our results show that prophages and gene transfer agents are significant sources of genomic diversity in roseobacter, with potential roles in the ecology of this globally distributed bacterial group.
Collapse
Affiliation(s)
- Kathryn Forcone
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
| | - Felipe H. Coutinho
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche, Aptdo. 18, Ctra. Alicante-Valencia, s/n, 03550 San Juan de Alicante, Spain;
| | - Giselle S. Cavalcanti
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
| | - Cynthia B. Silveira
- Department of Biology, University of Miami, 1301 Memorial Dr., Coral Gables, Miami, FL 33146, USA; (K.F.); (G.S.C.)
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149, USA
- Correspondence:
| |
Collapse
|
18
|
Chiba Y, Tomaru Y, Shimabukuro H, Kimura K, Hirai M, Takaki Y, Hagiwara D, Nunoura T, Urayama SI. Viral RNA Genomes Identified from Marine Macroalgae and a Diatom. Microbes Environ 2021; 35. [PMID: 32554943 PMCID: PMC7511793 DOI: 10.1264/jsme2.me20016] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Protists provide insights into the diversity and function of RNA viruses in marine systems. Among them, marine macroalgae are good targets for RNA virome analyses because they have a sufficient biomass in nature. However, RNA viruses in macroalgae have not yet been examined in detail, and only partial genome sequences have been reported for the majority of RNA viruses. Therefore, to obtain further insights into the distribution and diversity of RNA viruses associated with marine protists, we herein examined RNA viruses in macroalgae and a diatom. We report the putative complete genome sequences of six novel RNA viruses from two marine macroalgae and one diatom holobiont. Four viruses were not classified into established viral genera or families. Furthermore, a virus classified into Totiviridae showed a genome structure that has not yet been reported in this family. These results suggest that a number of distinct RNA viruses are widespread in a broad range of protists.
Collapse
Affiliation(s)
- Yuto Chiba
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba.,Faculty of Science, International College of Arts and Science, Yokohama City University
| | - Yuji Tomaru
- Japan Fisheries Research and Education Agency, National Research Institute of Fisheries and Environment of the Inland Sea
| | - Hiromori Shimabukuro
- Japan Fisheries Research and Education Agency, National Research Institute of Fisheries and Environment of the Inland Sea
| | | | - Miho Hirai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, JAMSTEC
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, JAMSTEC
| | - Daisuke Hagiwara
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba.,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Syun-Ichi Urayama
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba.,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba.,Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| |
Collapse
|
19
|
Luque A, Benler S, Lee DY, Brown C, White S. The Missing Tailed Phages: Prediction of Small Capsid Candidates. Microorganisms 2020; 8:E1944. [PMID: 33302408 PMCID: PMC7762592 DOI: 10.3390/microorganisms8121944] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/04/2020] [Accepted: 12/05/2020] [Indexed: 12/17/2022] Open
Abstract
Tailed phages are the most abundant and diverse group of viruses on the planet. Yet, the smallest tailed phages display relatively complex capsids and large genomes compared to other viruses. The lack of tailed phages forming the common icosahedral capsid architectures T = 1 and T = 3 is puzzling. Here, we extracted geometrical features from high-resolution tailed phage capsid reconstructions and built a statistical model based on physical principles to predict the capsid diameter and genome length of the missing small-tailed phage capsids. We applied the model to 3348 isolated tailed phage genomes and 1496 gut metagenome-assembled tailed phage genomes. Four isolated tailed phages were predicted to form T = 3 icosahedral capsids, and twenty-one metagenome-assembled tailed phages were predicted to form T < 3 capsids. The smallest capsid predicted was a T = 4/3 ≈ 1.33 architecture. No tailed phages were predicted to form the smallest icosahedral architecture, T = 1. We discuss the feasibility of the missing T = 1 tailed phage capsids and the implications of isolating and characterizing small-tailed phages for viral evolution and phage therapy.
Collapse
Affiliation(s)
- Antoni Luque
- Viral Information Institute, San Diego State University, San Diego, CA 92182, USA; (D.Y.L.); (C.B.)
- Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182, USA
| | - Sean Benler
- National Center for Biotechnology Information (NCBI), Bethesda, MD 20894, USA;
| | - Diana Y. Lee
- Viral Information Institute, San Diego State University, San Diego, CA 92182, USA; (D.Y.L.); (C.B.)
- Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA
| | - Colin Brown
- Viral Information Institute, San Diego State University, San Diego, CA 92182, USA; (D.Y.L.); (C.B.)
- Department of Physics, San Diego State University, San Diego, CA 92182, USA
| | - Simon White
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA;
| |
Collapse
|
20
|
Tuttle MJ, Buchan A. Lysogeny in the oceans: Lessons from cultivated model systems and a reanalysis of its prevalence. Environ Microbiol 2020; 22:4919-4933. [PMID: 32935433 DOI: 10.1111/1462-2920.15233] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/19/2020] [Accepted: 08/23/2020] [Indexed: 12/12/2022]
Abstract
In the oceans, viruses that infect bacteria (phages) influence a variety of microbially mediated processes that drive global biogeochemical cycles. The nature of their influence is dependent upon infection mode, be it lytic or lysogenic. Temperate phages are predicted to be prevalent in marine systems where they are expected to execute both types of infection modes. Understanding the range and outcomes of temperate phage-host interactions is fundamental for evaluating their ecological impact. Here, we (i) review phage-mediated rewiring of host metabolism, with a focus on marine systems, (ii) consider the range and nature of temperate phage-host interactions, and (iii) draw on studies of cultivated model systems to examine the consequences of lysogeny among several dominant marine bacterial lineages. We also readdress the prevalence of lysogeny among marine bacteria by probing a collection of 1239 publicly available bacterial genomes, representing cultured and uncultivated strains, for evidence of complete prophages. Our conservative analysis, anticipated to underestimate true prevalence, predicts 18% of the genomes examined contain at least one prophage, the majority (97%) were found within genomes of cultured isolates. These results highlight the need for cultivation of additional model systems to better capture the diversity of temperate phage-host interactions in the oceans.
Collapse
Affiliation(s)
- Matthew J Tuttle
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| |
Collapse
|
21
|
Quantification of Lysogeny Caused by Phage Coinfections in Microbial Communities from Biophysical Principles. mSystems 2020; 5:5/5/e00353-20. [PMID: 32934113 PMCID: PMC7498681 DOI: 10.1128/msystems.00353-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The association of temperate phages and bacterial hosts during lysogeny manipulates microbial dynamics from the oceans to the human gut. Lysogeny is well studied in laboratory models, but its environmental drivers remain unclear. Here, we quantified the probability of lysogenization caused by phage coinfections, a well-known trigger of lysogeny, in marine and gut microbial environments. Coinfections were quantified by developing a biophysical model that incorporated the traits of viral and bacterial communities. Lysogenization via coinfection was more frequent in highly productive environments like the gut, due to higher microbial densities and higher phage adsorption rates. At low cell densities, lysogenization occurred in bacteria with long duplication times. These results bridge the molecular understanding of lysogeny with the ecology of complex microbial communities. Temperate phages can associate with their bacterial host to form a lysogen, often modifying the phenotype of the host. Lysogens are dominant in the microbially dense environment of the mammalian gut. This observation contrasts with the long-standing hypothesis of lysogeny being favored at low microbial densities, such as in oligotrophic marine environments. Here, we hypothesized that phage coinfections—a well-understood molecular mechanism of lysogenization—increase at high microbial abundances. To test this hypothesis, we developed a biophysical model of coinfection for marine and gut microbiomes. The model stochastically sampled ranges of phage and bacterial concentrations, adsorption rates, lysogenic commitment times, and community diversity from each environment. In 90% of the sampled marine communities, less than 10% of the bacteria were predicted to be lysogenized via coinfection. In contrast, 25% of the sampled gut communities displayed more than 25% of lysogenization. The probability of lysogenization in the gut was a consequence of the higher densities and higher adsorption rates. These results suggest that, on average, coinfections can form two trillion lysogens in the human gut every day. In marine microbiomes, which were characterized by lower densities and phage adsorption rates, lysogeny via coinfection was still possible for communities with long lysogenic commitment times. Our study indicates that different physical factors causing coinfections can reconcile the traditional view of lysogeny at poor host growth (long commitment times) and the recent Piggyback-the-Winner framework proposing that lysogeny is favored in rich environments (high densities and adsorption rates). IMPORTANCE The association of temperate phages and bacterial hosts during lysogeny manipulates microbial dynamics from the oceans to the human gut. Lysogeny is well studied in laboratory models, but its environmental drivers remain unclear. Here, we quantified the probability of lysogenization caused by phage coinfections, a well-known trigger of lysogeny, in marine and gut microbial environments. Coinfections were quantified by developing a biophysical model that incorporated the traits of viral and bacterial communities. Lysogenization via coinfection was more frequent in highly productive environments like the gut, due to higher microbial densities and higher phage adsorption rates. At low cell densities, lysogenization occurred in bacteria with long duplication times. These results bridge the molecular understanding of lysogeny with the ecology of complex microbial communities.
Collapse
|
22
|
Mauritzen JJ, Castillo D, Tan D, Svenningsen SL, Middelboe M. Beyond Cholera: Characterization of zot-Encoding Filamentous Phages in the Marine Fish Pathogen Vibrio anguillarum. Viruses 2020; 12:v12070730. [PMID: 32640584 PMCID: PMC7412436 DOI: 10.3390/v12070730] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/29/2020] [Accepted: 07/02/2020] [Indexed: 12/22/2022] Open
Abstract
Zonula occludens toxin (Zot) is a conserved protein in filamentous vibriophages and has been reported as a putative toxin in Vibrio cholerae. Recently, widespread distribution of zot-encoding prophages was found among marine Vibrio species, including environmental isolates. However, little is known about the dynamics of these prophages beyond V. cholerae. In this study, we characterized and quantified the zot-encoding filamentous phage VAIϕ, spontaneously induced from the fish pathogen V. anguillarum. VAIϕ contained 6117 bp encoding 11 ORFs, including ORF8pVAI, exhibiting 27%–73% amino acid identity to Inovirus Zot-like proteins. A qPCR method revealed an average of four VAIϕ genomes per host genome during host exponential growth phase, and PCR demonstrated dissemination of induced VAIϕ to other V. anguillarum strains through re-integration in non-lysogens. VAIϕ integrated into both chromosomes of V. anguillarum by recombination, causing changes in a putative ORF in the phage genome. Phylogenetic analysis of the V. anguillarumInoviridae elements revealed mosaic genome structures related to mainly V. cholerae. Altogether, this study contributes to the understanding of Inovirus infection dynamics and mobilization of zot-like genes beyond human pathogenic vibrios, and discusses their potential role in the evolution of the fish pathogen V. anguillarum.
Collapse
Affiliation(s)
- Jesper Juel Mauritzen
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (J.J.M.); (D.C.)
| | - Daniel Castillo
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (J.J.M.); (D.C.)
| | - Demeng Tan
- Section for Biomolecular Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200 København N, Denmark; (D.T.); (S.L.S.)
| | - Sine Lo Svenningsen
- Section for Biomolecular Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200 København N, Denmark; (D.T.); (S.L.S.)
| | - Mathias Middelboe
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (J.J.M.); (D.C.)
- Correspondence: ; Tel.: +45-35-32-19-91
| |
Collapse
|