1
|
Cook R, Brown N, Rihtman B, Michniewski S, Redgwell T, Clokie M, Stekel DJ, Chen Y, Scanlan DJ, Hobman JL, Nelson A, Jones MA, Smith D, Millard A. The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies. Microb Genom 2024; 10:001198. [PMID: 38376377 PMCID: PMC10926689 DOI: 10.1099/mgen.0.001198] [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: 02/25/2023] [Accepted: 01/25/2024] [Indexed: 02/21/2024] Open
Abstract
Viral metagenomics has fuelled a rapid change in our understanding of global viral diversity and ecology. Long-read sequencing and hybrid assembly approaches that combine long- and short-read technologies are now being widely implemented in bacterial genomics and metagenomics. However, the use of long-read sequencing to investigate viral communities is still in its infancy. While Nanopore and PacBio technologies have been applied to viral metagenomics, it is not known to what extent different technologies will impact the reconstruction of the viral community. Thus, we constructed a mock bacteriophage community of previously sequenced phage genomes and sequenced them using Illumina, Nanopore and PacBio sequencing technologies and tested a number of different assembly approaches. When using a single sequencing technology, Illumina assemblies were the best at recovering phage genomes. Nanopore- and PacBio-only assemblies performed poorly in comparison to Illumina in both genome recovery and error rates, which both varied with the assembler used. The best Nanopore assembly had errors that manifested as SNPs and INDELs at frequencies 41 and 157 % higher than found in Illumina only assemblies, respectively. While the best PacBio assemblies had SNPs at frequencies 12 and 78 % higher than found in Illumina-only assemblies, respectively. Despite high-read coverage, long-read-only assemblies recovered a maximum of one complete genome from any assembly, unless reads were down-sampled prior to assembly. Overall the best approach was assembly by a combination of Illumina and Nanopore reads, which reduced error rates to levels comparable with short-read-only assemblies. When using a single technology, Illumina only was the best approach. The differences in genome recovery and error rates between technology and assembler had downstream impacts on gene prediction, viral prediction, and subsequent estimates of diversity within a sample. These findings will provide a starting point for others in the choice of reads and assembly algorithms for the analysis of viromes.
Collapse
Affiliation(s)
- Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Nathan Brown
- Centre for Phage Research, Dept Genetics and Genome Biology, University of Leicester, University Road, Leicester, Leicestershire, LE1 7RH, UK
| | - Branko Rihtman
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Slawomir Michniewski
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Tamsin Redgwell
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820, Gentofte, Denmark
| | - Martha Clokie
- Centre for Phage Research, Dept Genetics and Genome Biology, University of Leicester, University Road, Leicester, Leicestershire, LE1 7RH, UK
| | - Dov J. Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
- Department of Mathematics and Applied Mathematics, University of Johannesburg, Rossmore 2029, South Africa
| | - Yin Chen
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - David J. Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Jon L. Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Andrew Nelson
- Faculty of Health and Life Sciences, University of Northumbria, Newcastle upon Tyne, NE1 8ST, UK
| | - Michael A. Jones
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough, Leicestershire, LE12 5RD, UK
| | - Darren Smith
- Faculty of Health and Life Sciences, University of Northumbria, Newcastle upon Tyne, NE1 8ST, UK
| | - Andrew Millard
- Centre for Phage Research, Dept Genetics and Genome Biology, University of Leicester, University Road, Leicester, Leicestershire, LE1 7RH, UK
| |
Collapse
|
2
|
Xiong L, Li Y, Zeng K, Wei Y, Li H, Ji X. Revealing viral diversity in the Napahai plateau wetland based on metagenomics. Antonie Van Leeuwenhoek 2023; 117:3. [PMID: 38153618 DOI: 10.1007/s10482-023-01912-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/22/2023] [Indexed: 12/29/2023]
Abstract
We focused on exploring the diversity of viruses in the Napahai plateau wetland, a unique ecosystem located in Yunnan, China. While viruses in marine environments have been extensively studied for their influence on microbial metabolism and biogeochemical cycles, little is known about their composition and function in plateau wetlands. Metagenomic analysis was employed to investigate the viral diversity and biogeochemical impacts in the Napahai wetland. It revealed that the Caudoviricetes and Malgrandaviricetes class level was the most abundant viral category based on phylogenetic analysis. Additionally, a gene-sharing network highlighted the presence of numerous unexplored viruses and demonstrated their unique characteristics and significant variation within the viral community of the Napahai wetland. Furthermore, the study identified the auxiliary metabolic genes (AMGs). AMGs provide phages with additional functions, such as protection against host degradation and involvement in metabolic pathways, such as the pentose phosphate pathway and DNA biosynthesis. The viruses in the Napahai wetland were found to influence carbon, nitrogen, sulfur, and amino acid metabolism, indirectly contributing to biogeochemical cycling through these AMGs. Overall, the research sheds light on the diverse and unique viral communities in the Napahai plateau wetland and emphasizes the significant roles of viruses in microbial ecology. The findings contribute to a deeper understanding of the characteristics and ecological functions of viral communities in plateau wetland ecosystems.
Collapse
Affiliation(s)
- Lingling Xiong
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yanmei Li
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Kun Zeng
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Yunlin Wei
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Haiyan Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Xiuling Ji
- Faculty of Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
| |
Collapse
|
3
|
Gonzalez-Serrano R, Rosselli R, Roda-Garcia JJ, Martin-Cuadrado AB, Rodriguez-Valera F, Dunne M. Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps. Nat Commun 2023; 14:6517. [PMID: 37845226 PMCID: PMC10579305 DOI: 10.1038/s41467-023-42114-8] [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: 02/20/2023] [Accepted: 09/27/2023] [Indexed: 10/18/2023] Open
Abstract
The host recognition modules encoding the injection machinery and receptor binding proteins (RBPs) of bacteriophages are predisposed to mutation and recombination to maintain infectivity towards co-evolving bacterial hosts. In this study, we reveal how Alteromonas mediterranea schitovirus A5 shares its host recognition module, including tail fiber and cognate chaperone, with phages from distantly related families including Alteromonas myovirus V22. While the V22 chaperone is essential for producing active tail fibers, here we demonstrate production of functional A5 tail fibers regardless of chaperone co-expression. AlphaFold-generated models of tail fiber and chaperone pairs from phages A5, V22, and other Alteromonas phages reveal how amino acid insertions within both A5-like proteins results in a knob domain duplication in the tail fiber and a chaperone β-hairpin "tentacle" extension. These structural modifications are linked to differences in chaperone dependency between the A5 and V22 tail fibers. Structural similarity between the chaperones and intramolecular chaperone domains of other phage RBPs suggests an additional function of these chaperones as transient fiber "caps". Finally, our identification of homologous host recognition modules from morphologically distinct phages implies that horizontal gene transfer and recombination events between unrelated phages may be a more common process than previously thought among Caudoviricetes phages.
Collapse
Affiliation(s)
- Rafael Gonzalez-Serrano
- Evolutionary Genomics Group, Universidad Miguel Hernández, San Juan de Alicante, Spain
- Centro de Biología Molecular Severo Ochoa, CBMSO-CSIC, Madrid, Spain
| | - Riccardo Rosselli
- Research & Development Department, LABAQUA S.A. Las Atalayas, Alicante, Spain
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Juan J Roda-Garcia
- Evolutionary Genomics Group, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | | | | | - Matthew Dunne
- Institute of Food, Nutrition and Health, ETH Zurich, Switzerland.
| |
Collapse
|
4
|
Ma R, Chen X, Li Y, Jiao N, Zhang R. Diversity, evolution and life strategies of CbK-like phages. Environ Microbiol 2023. [PMID: 36807729 DOI: 10.1111/1462-2920.16354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023]
Abstract
Caulobacter phage CbK has been extensively studied as a model system in virology and bacteriology. Lysogeny-related genes have been found in each CbK-like isolate, suggesting a life strategy of both lytic and lysogenic cycles. However, whether CbK-related phages can enter lysogeny is still undetermined. This study identified new CbK-like sequences and expanded the collection of CbK-related phages. A common ancestry with a temperate lifestyle was predicted for the group, however, which subsequently evolved into two clades of different genome sizes and host associations. Through the examination of phage recombinase genes, alignment of attachment sites on the phage and bacterial genomes (attP-attB pairing), and the experimental validation, different lifestyles were found among the different members. A majority of clade II members retain a lysogenic lifestyle, whereas all clade I members have evolved into an obligate lytic lifestyle via a loss of the gene encoding Cre-like recombinase and the coupled attP fragment. We postulated that the loss of lysogeny may be a by-product of the increase in phage genome size, and vice versa. Clade I is likely to overcome the costs through maintaining more auxiliary metabolic genes (AMGs), particularly for those involved in protein metabolism, to strengthen host takeover and further benefit virion production.
Collapse
Affiliation(s)
- Ruijie Ma
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yingying Li
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| |
Collapse
|
5
|
Doss JH, Barekzi N, Gauthier DT. Improving high-throughput techniques for bacteriophage discovery in multi-well plates. METHODS IN MICROBIOLOGY 2022; 200:106542. [PMID: 35882287 DOI: 10.1016/j.mimet.2022.106542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/21/2022] [Accepted: 07/16/2022] [Indexed: 10/16/2022]
Abstract
Bacteriophages (also called phages) are viruses of bacteria that have numerous applications in medicine, agriculture, ecology, and molecular biology. With the increasing interest in phages for their many uses, it is now especially important to make phage discovery more efficient and economical. Using the host Mycobacterium smegmatis mc2155, which is a model organism for phage discovery research and is closely related to important pathogens of humans and other animals, we investigated three procedures that are an integral part of phage discovery: enrichment of environmental samples, phage isolation and detection (which can also be used for host range determination), and phage purification. Enrichment in 6-well plates was successful with most environmental samples, and enrichment in 24- and 96-well plates was successful with some environmental samples, demonstrating that larger sample volumes are preferred when possible, but smaller sample volumes may be acceptable if the starting concentration of phages is sufficiently high. Measuring absorbance in multi-well plates was at least as sensitive as the traditional plaque assay for the detection of phages. We also demonstrated a technique for the purification of single phage types from mixed cultures in liquid medium. Multi-well techniques can be used as alternatives or complementary approaches to traditional methods of phage discovery and characterization depending on the needs of the researcher in terms of time, available resources, host species, phage-bacteria matches, and specific goals. In the future, these techniques could be applied to the discovery of phages of aquatic mycobacteria and other hosts for which few phages have currently been isolated.
Collapse
Affiliation(s)
- Janis H Doss
- The Association of Public Health Laboratories, Silver Spring, MD, USA.
| | - Nazir Barekzi
- Department of Biology, Norfolk State University, Norfolk, VA, USA.
| | - David T Gauthier
- Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA.
| |
Collapse
|
6
|
Skliros D, Karpouzis E, Kalloniati C, Katharios P, Flemetakis E. Comparative genomic analysis of dwarf Vibrio myoviruses defines a conserved gene cluster for successful phage infection. Arch Virol 2022; 167:501-516. [PMID: 35000006 DOI: 10.1007/s00705-021-05340-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 11/08/2021] [Indexed: 11/30/2022]
Abstract
Tailed bacteriophages have been at the center of attention, not only for their ability to infect and kill pathogenic bacteria but also due to their peculiar and intriguing complex contractile tail structure. Tailed bacteriophages with contractile tails are known to have a Myoviridae morphotype and are members of the order Caudovirales. Large bacteriophages with a genome larger than 150 kbp have been studied for their ability to use multiple infection and lysis strategies to replicate more efficiently. On the other hand, smaller bacteriophages with fewer genes are represented in the GenBank database in greater numbers, and have several genes with unknown function. Isolation and molecular characterization of a newly reported bacteriophage named Athena1 revealed that it is a strongly lytic bacteriophage with a genome size of 39,826 bp. This prompted us to perform a comparative genomic analysis of Vibrio myoviruses with a genome size of no more than 50 kbp. The results revealed a pattern of genomic organization that includes sets of genes responsible for virion morphogenesis, replication/recombination of DNA, and lysis/lysogeny switching. By studying phylogenetic gene markers, we were able to draw conclusions about evolutionary events that shaped the genomic mosaicism of these phages, pinpointing the importance of a conserved organization of the genomic region encoding the baseplate protein for successful infection of Gram-negative bacteria. In addition, we propose the creation of new genera for dwarf Vibrio myoviruses. Comparative genomics of phages infecting aquatic bacteria could provide information that is useful for combating fish pathogens in aquaculture, using novel strategies.
Collapse
Affiliation(s)
- Dimitrios Skliros
- Laboratory of Molecular Biology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Efthymios Karpouzis
- Laboratory of Molecular Biology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Chrysanthi Kalloniati
- Laboratory of Molecular Biology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology, and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece. .,EU-CONEXUS European University, Athens, Greece.
| |
Collapse
|
7
|
Cook R, Brown N, Redgwell T, Rihtman B, Barnes M, Clokie M, Stekel DJ, Hobman J, Jones MA, Millard A. INfrastructure for a PHAge REference Database: Identification of Large-Scale Biases in the Current Collection of Cultured Phage Genomes. PHAGE (NEW ROCHELLE, N.Y.) 2021; 2:214-223. [PMID: 36159887 PMCID: PMC9041510 DOI: 10.1089/phage.2021.0007] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Background: With advances in sequencing technology and decreasing costs, the number of phage genomes that have been sequenced has increased markedly in the past decade. Materials and Methods: We developed an automated retrieval and analysis system for phage genomes (https://github.com/RyanCook94/inphared) to produce the INfrastructure for a PHAge REference Database (INPHARED) of phage genomes and associated metadata. Results: As of January 2021, 14,244 complete phage genomes have been sequenced. The INPHARED data set is dominated by phages that infect a small number of bacterial genera, with 75% of phages isolated on only 30 bacterial genera. There is further bias, with significantly more lytic phage genomes (∼70%) than temperate (∼30%) within our database. Collectively, this results in ∼54% of temperate phage genomes originating from just three host genera. With much debate on the carriage of antibiotic resistance genes and their potential safety in phage therapy, we searched for putative antibiotic resistance genes. Frequency of antibiotic resistance gene carriage was found to be higher in temperate phages than in lytic phages and again varied with host. Conclusions: Given the bias of currently sequenced phage genomes, we suggest to fully understand phage diversity, efforts should be made to isolate and sequence a larger number of phages, in particular temperate phages, from a greater diversity of hosts.
Collapse
Affiliation(s)
- Ryan Cook
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom
| | - Nathan Brown
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Tamsin Redgwell
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Branko Rihtman
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Megan Barnes
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Martha Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Dov J. Stekel
- School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Jon Hobman
- School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Michael A. Jones
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom.,Address correspondence to: Andrew Millard, PhD, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, Leicestershire LE1 7RH, United Kingdom
| |
Collapse
|
8
|
Vladimirov M, Gautam V, Davidson AR. Identification of the tail assembly chaperone genes of T4-Like phages suggests a mechanism other than translational frameshifting for biogenesis of their encoded proteins. Virology 2021; 566:9-15. [PMID: 34826709 DOI: 10.1016/j.virol.2021.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 11/29/2022]
Abstract
Tape measure (TM) proteins are essential for the formation of long-tailed phages. TM protein assembly into tails requires the action of tail assembly chaperones (TACs). TACs (e.g. gpG and gpT of E. coli phage lambda) are usually produced in a short (TAC-N) and long form (TAC-NC) with the latter comprised of TAC-N with an additional C-terminal domain (TAC-C). TAC-NC is generally synthesized through a ribosomal frameshifting mechanism. TAC encoding genes have never been identified in the intensively studied Escherichia coli phage T4, or any related phages. Here, we have bioinformatically identified putative TAC encoding genes in diverse T4-like phage genomes. The frameshifting mechanism for producing TAC-NC appears to be conserved in several T4-like phage groups. However, the group including phage T4 itself likely employs a different strategy whereby TAC-N and TAC-NC are encoded by separate genes (26 and 51 in phage T4).
Collapse
Affiliation(s)
- Maria Vladimirov
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Vasu Gautam
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alan R Davidson
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
9
|
Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts. THE ISME JOURNAL 2021; 15:3129-3147. [PMID: 33972727 PMCID: PMC8528832 DOI: 10.1038/s41396-021-00989-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 03/08/2021] [Accepted: 04/14/2021] [Indexed: 02/03/2023]
Abstract
The marine picoeukaryote Bathycoccus prasinos has been considered a cosmopolitan alga, although recent studies indicate two ecotypes exist, Clade BI (B. prasinos) and Clade BII. Viruses that infect Bathycoccus Clade BI are known (BpVs), but not that infect BII. We isolated three dsDNA prasinoviruses from the Sargasso Sea against Clade BII isolate RCC716. The BII-Vs do not infect BI, and two (BII-V2 and BII-V3) have larger genomes (~210 kb) than BI-Viruses and BII-V1. BII-Vs share ~90% of their proteins, and between 65% to 83% of their proteins with sequenced BpVs. Phylogenomic reconstructions and PolB analyses establish close-relatedness of BII-V2 and BII-V3, yet BII-V2 has 10-fold higher infectivity and induces greater mortality on host isolate RCC716. BII-V1 is more distant, has a shorter latent period, and infects both available BII isolates, RCC716 and RCC715, while BII-V2 and BII-V3 do not exhibit productive infection of the latter in our experiments. Global metagenome analyses show Clade BI and BII algal relative abundances correlate positively with their respective viruses. The distributions delineate BI/BpVs as occupying lower temperature mesotrophic and coastal systems, whereas BII/BII-Vs occupy warmer temperature, higher salinity ecosystems. Accordingly, with molecular diagnostic support, we name Clade BII Bathycoccus calidus sp. nov. and propose that molecular diversity within this new species likely connects to the differentiated host-virus dynamics observed in our time course experiments. Overall, the tightly linked biogeography of Bathycoccus host and virus clades observed herein supports species-level host specificity, with strain-level variations in infection parameters.
Collapse
|
10
|
Shang J, Jiang J, Sun Y. Bacteriophage classification for assembled contigs using graph convolutional network. Bioinformatics 2021; 37:i25-i33. [PMID: 34252923 PMCID: PMC8275337 DOI: 10.1093/bioinformatics/btab293] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Motivation Bacteriophages (aka phages), which mainly infect bacteria, play key roles in the biology of microbes. As the most abundant biological entities on the planet, the number of discovered phages is only the tip of the iceberg. Recently, many new phages have been revealed using high-throughput sequencing, particularly metagenomic sequencing. Compared to the fast accumulation of phage-like sequences, there is a serious lag in taxonomic classification of phages. High diversity, abundance and limited known phages pose great challenges for taxonomic analysis. In particular, alignment-based tools have difficulty in classifying fast accumulating contigs assembled from metagenomic data. Results In this work, we present a novel semi-supervised learning model, named PhaGCN, to conduct taxonomic classification for phage contigs. In this learning model, we construct a knowledge graph by combining the DNA sequence features learned by convolutional neural network and protein sequence similarity gained from gene-sharing network. Then we apply graph convolutional network to utilize both the labeled and unlabeled samples in training to enhance the learning ability. We tested PhaGCN on both simulated and real sequencing data. The results clearly show that our method competes favorably against available phage classification tools. Availability and implementation The source code of PhaGCN is available via: https://github.com/KennthShang/PhaGCN.
Collapse
Affiliation(s)
- Jiayu Shang
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong (SAR), China
| | - Jingzhe Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong Province, China
| | - Yanni Sun
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong (SAR), China
| |
Collapse
|
11
|
Gazitúa MC, Vik DR, Roux S, Gregory AC, Bolduc B, Widner B, Mulholland MR, Hallam SJ, Ulloa O, Sullivan MB. Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters. THE ISME JOURNAL 2021; 15:981-998. [PMID: 33199808 PMCID: PMC8115048 DOI: 10.1038/s41396-020-00825-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 09/30/2020] [Accepted: 10/27/2020] [Indexed: 01/29/2023]
Abstract
Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.
Collapse
Affiliation(s)
- M. Consuelo Gazitúa
- grid.261331.40000 0001 2285 7943Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA ,Viromica Consulting, Santiago, Chile
| | - Dean R. Vik
- grid.261331.40000 0001 2285 7943Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA
| | - Simon Roux
- grid.451309.a0000 0004 0449 479XDOE Joint Genome Institute, Berkeley, CA USA
| | - Ann C. Gregory
- grid.261331.40000 0001 2285 7943Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA
| | - Benjamin Bolduc
- grid.261331.40000 0001 2285 7943Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA
| | - Brittany Widner
- grid.261368.80000 0001 2164 3177Department of Ocean, Earth and Atmospheric Sciences, Old Dominion University, Norfolk, VA USA ,grid.56466.370000 0004 0504 7510Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - Margaret R. Mulholland
- grid.261368.80000 0001 2164 3177Department of Ocean, Earth and Atmospheric Sciences, Old Dominion University, Norfolk, VA USA
| | - Steven J. Hallam
- grid.17091.3e0000 0001 2288 9830Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC Canada
| | - Osvaldo Ulloa
- grid.5380.e0000 0001 2298 9663Departamento de Oceanografía & Instituto Milenio de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - Matthew B. Sullivan
- grid.261331.40000 0001 2285 7943Department of Microbiology, The Ohio State University, Columbus, OH 43210 USA ,grid.261331.40000 0001 2285 7943Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH USA
| |
Collapse
|
12
|
Huang X, Jiao N, Zhang R. The genomic content and context of auxiliary metabolic genes in roseophages. Environ Microbiol 2021; 23:3743-3757. [PMID: 33511765 DOI: 10.1111/1462-2920.15412] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/24/2021] [Indexed: 11/26/2022]
Abstract
Marine bacteriophages frequently possess auxiliary metabolic genes (AMGs) that accelerate host metabolism during phage infection. The significance of AMGs in phage infecting the ecologically important Roseobacter clade, found predominantly in marine environments, remains to be determined. Here, we analysed the distribution and genomic context of 180 AMGs, annotated into 20 types, across 50 roseophage genomes. Roseophages share seven high-frequency AMGs (trx, grx, RNR, thyX, DCD, phoH, and mazG), most of them involved in the nucleotide biosynthesis pathway that represent conserved intra and inter operational taxonomic units (OTUs), and share ≥97% full-length DNA sequence similarity. Sporadic AMGs (dUTPase, lexA, degS, Que, NAPRT, AHL, pcnB, ctrA, RTX, RNR-nrdA, RNR-nrdE, wclP, and flgJ), present in only one or two OTUs, show high functional diversity. The roseophage AMG repertoire weakly correlates with environmental factors, while host range partially explains the sporadic AMG distribution. Locally co-linear blocks distribution index (LDI) analysis indicated that high-frequency roseopodovirus AMGs are restricted to particular genomic islands, possibly originating from limited historical acquisition events. Low-frequency roseopodovirus AMGs and all roseosiphovirus AMGs have high LDI values, implying multiple historical acquisition events. In summary, roseophages have acquired a range of AMGs through horizontal gene transfer, and the forces shaping the evolution of roseophages are described.
Collapse
Affiliation(s)
- Xingyu Huang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean & Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean & Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean & Earth Sciences, Xiamen University, Xiamen, 361102, China
| |
Collapse
|
13
|
Cibulski S, Alves de Lima D, Fernandes Dos Santos H, Teixeira TF, Tochetto C, Mayer FQ, Roehe PM. A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil. Virology 2021; 552:1-9. [PMID: 33032031 PMCID: PMC7521440 DOI: 10.1016/j.virol.2020.09.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/12/2020] [Accepted: 09/13/2020] [Indexed: 02/08/2023]
Abstract
A viral metagenomics study was conducted in beef, pork, and chicken sold in supermarkets from Southern Brazil. From chicken, six distinct gyroviruses (GyV) were detected, including GyV3 and GyV6, which for the first time were detected in samples from avian species, plus a novel smacovirus species and two highly divergent circular Rep-encoding ssDNA (CRESS-DNA) viruses. From pork, genomes of numerous anelloviruses, porcine parvovirus 5 (PPV5) and 6 (PPV6), two new genomoviruses and two new CRESS-DNA viruses were found. Finally, two new CRESS-DNA genomes were recovered from beef. Although none of these viruses have history of transmission to humans, the findings reported here reveal that such agents are inevitably consumed in diets that include these types of meat.
Collapse
Affiliation(s)
- Samuel Cibulski
- Centro de Biotecnologia - CBiotec, Laboratório de Biotecnologia Celular e Molecular, Universidade Federal da Paraíba - UFPB, João Pessoa, Paraíba, Brazil.
| | - Diane Alves de Lima
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil; Centro Universitário da Serra Gaúcha - FSG, Caxias do Sul, Grande do Sul, Brazil
| | - Helton Fernandes Dos Santos
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria - UFSM, Santa Maria, Rio Grande do Sul, Brazil
| | - Thais Fumaco Teixeira
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, RS, Brazil
| | - Caroline Tochetto
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, RS, Brazil
| | - Paulo Michel Roehe
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| |
Collapse
|
14
|
Characterization and Genome Analysis of a Novel Mu-like Phage VW-6B Isolated from the Napahai Plateau Wetland of China. Curr Microbiol 2020; 78:150-158. [PMID: 33150466 DOI: 10.1007/s00284-020-02277-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 10/27/2020] [Indexed: 10/23/2022]
Abstract
Although bacteriophages are more numerous and have smaller genomes than their bacterial hosts, relatively few have their genomes sequenced. Here, we isolated the Pseudomonas fluorescens bacteriophage from Napahai plateau wetland and performed de novo genome sequencing. Based on the previous biological characteristics and bioinformatics analysis, it was determined that VW-6B was a linear double-stranded DNA (dsDNA) phage with 35,306 bp, with 56.76% G+C content and 197 bp tandem repeats. The VW-6B genome contained 46 open-reading frames (ORFs), and no tRNA genes were found. Based on phage genome structure, sequence comparison, and collinear analysis, VW-6B should be classified into the family Siphoviridae and be considered as a member of a new species in the Mu-like phage. The newly isolated bacteriophage can specifically infect P. fluorescens, which further enriches the diversity of known bacteriophages and provides a basis for the subsequent research and application of bacteriophages.
Collapse
|
15
|
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
|
16
|
Alteromonas Myovirus V22 Represents a New Genus of Marine Bacteriophages Requiring a Tail Fiber Chaperone for Host Recognition. mSystems 2020; 5:5/3/e00217-20. [PMID: 32518192 PMCID: PMC7289586 DOI: 10.1128/msystems.00217-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Marine phages play a variety of critical roles in regulating the microbial composition of our oceans. Despite constituting the majority of genetic diversity within these environments, there are relatively few isolates with complete genome sequences or in-depth analyses of their host interaction mechanisms, such as characterization of their receptor binding proteins (RBPs). Here, we present the 92,760-bp genome of the Alteromonas-targeting phage V22. Genomic and morphological analyses identify V22 as a myovirus; however, due to a lack of sequence similarity to any other known myoviruses, we propose that V22 be classified as the type phage of a new Myoalterovirus genus within the Myoviridae family. V22 shows gene homology and synteny with two different subfamilies of phages infecting enterobacteria, specifically within the structural region of its genome. To improve our understanding of the V22 adsorption process, we identified putative RBPs (gp23, gp24, and gp26) and tested their ability to decorate the V22 propagation strain, Alteromonas mediterranea PT11, as recombinant green fluorescent protein (GFP)-tagged constructs. Only GFP-gp26 was capable of bacterial recognition and identified as the V22 RBP. Interestingly, production of functional GFP-gp26 required coexpression with the downstream protein gp27. GFP-gp26 could be expressed alone but was incapable of host recognition. By combining size-exclusion chromatography with fluorescence microscopy, we reveal how gp27 is not a component of the final RBP complex but instead is identified as a new type of phage-encoded intermolecular chaperone that is essential for maturation of the gp26 RBP.IMPORTANCE Host recognition by phage-encoded receptor binding proteins (RBPs) constitutes the first step in all phage infections and the most critical determinant of host specificity. By characterizing new types of RBPs and identifying their essential chaperones, we hope to expand the repertoire of known phage-host recognition machineries. Due to their genetic plasticity, studying RBPs and their associated chaperones can shed new light onto viral evolution affecting phage-host interactions, which is essential for fields such as phage therapy or biotechnology. In addition, since marine phages constitute one of the most important reservoirs of noncharacterized genetic diversity on the planet, their genomic and functional characterization may be of paramount importance for the discovery of novel genes with potential applications.
Collapse
|
17
|
Dead or alive: sediment DNA archives as tools for tracking aquatic evolution and adaptation. Commun Biol 2020; 3:169. [PMID: 32265485 PMCID: PMC7138834 DOI: 10.1038/s42003-020-0899-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/10/2020] [Indexed: 12/18/2022] Open
Abstract
DNA can be preserved in marine and freshwater sediments both in bulk sediment and in intact, viable resting stages. Here, we assess the potential for combined use of ancient, environmental, DNA and timeseries of resurrected long-term dormant organisms, to reconstruct trophic interactions and evolutionary adaptation to changing environments. These new methods, coupled with independent evidence of biotic and abiotic forcing factors, can provide a holistic view of past ecosystems beyond that offered by standard palaeoecology, help us assess implications of ecological and molecular change for contemporary ecosystem functioning and services, and improve our ability to predict adaptation to environmental stress. Ellegaard et al. discuss the potential for using ancient environmental DNA (eDNA), combined with resurrection ecology, to analyse trophic interactions and evolutionary adaptation to changing environments. Their Review suggests that these techniques will improve our ability to predict genetic and phenotypic adaptation to environmental stress.
Collapse
|
18
|
Iranzo J, Faure G, Wolf YI, Koonin EV. Game-Theoretical Modeling of Interviral Conflicts Mediated by Mini-CRISPR Arrays. Front Microbiol 2020; 11:381. [PMID: 32265856 PMCID: PMC7099407 DOI: 10.3389/fmicb.2020.00381] [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: 11/13/2019] [Accepted: 02/20/2020] [Indexed: 12/30/2022] Open
Abstract
All cellular organisms coevolve with multiple viruses, so that both virus-host and intervirus conflicts are major factors of evolution. Accordingly, hosts evolve multiple, elaborate defense systems and viruses respond by evolving means of antidefense. Although less thoroughly characterized, several dedicated mechanisms of intervirus competition have been described as well. Recently, the genomes of some bacterial and archaeal viruses have been shown to harbor CRISPR mini-arrays that typically contain a single spacer targeting a closely related virus. The involvement of mini-arrays in an intervirus conflict has been experimentally demonstrated for a pair of archaeal viruses. We model the evolution of virus-encoded CRISPR mini-arrays using a game theoretical approach. Analysis of the model reveals multiple equilibria that include mutual targeting, unidirectional targeting, no targeting, cyclic polymorphism, and bistability. The choice between these evolutionary regimes depends on the model parameters including the coinfection frequency, differential productivity of the conflicting viruses, and the fitness cost of mini-arrays. At high coinfection frequencies, the model becomes a version of the Prisoner’s dilemma in which defection, i.e., mutual targeting between the competing viruses, is the winning strategy.
Collapse
Affiliation(s)
- Jaime Iranzo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain.,Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
19
|
Divya Ganeshan S, Hosseinidoust Z. Phage Therapy with a Focus on the Human Microbiota. Antibiotics (Basel) 2019; 8:E131. [PMID: 31461990 PMCID: PMC6783874 DOI: 10.3390/antibiotics8030131] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/14/2019] [Accepted: 08/23/2019] [Indexed: 01/12/2023] Open
Abstract
Bacteriophages are viruses that infect bacteria. After their discovery in the early 1900s, bacteriophages were a primary cure against infectious disease for almost 25 years, before being completely overshadowed by antibiotics. With the rise of antibiotic resistance, bacteriophages are being explored again for their antibacterial activity. One of the critical apprehensions regarding bacteriophage therapy, however, is the possibility of genome evolution, development of phage resistance, and subsequent perturbations to our microbiota. Through this review, we set out to explore the principles supporting the use of bacteriophages as a therapeutic agent, discuss the human gut microbiome in relation to the utilization of phage therapy, and the co-evolutionary arms race between host bacteria and phage in the context of the human microbiota.
Collapse
Affiliation(s)
| | - Zeinab Hosseinidoust
- School of Biomedical Engineering, McMaster University, Hamilton, ON L8S 4K1, Canada.
- Department of Chemical Engineering, McMaster University, Hamilton, ON L8S 4L7, Canada.
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S 4K1, Canada.
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada.
| |
Collapse
|
20
|
Batinovic S, Wassef F, Knowler SA, Rice DTF, Stanton CR, Rose J, Tucci J, Nittami T, Vinh A, Drummond GR, Sobey CG, Chan HT, Seviour RJ, Petrovski S, Franks AE. Bacteriophages in Natural and Artificial Environments. Pathogens 2019; 8:pathogens8030100. [PMID: 31336985 PMCID: PMC6789717 DOI: 10.3390/pathogens8030100] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 02/07/2023] Open
Abstract
Bacteriophages (phages) are biological entities that have attracted a great deal of attention in recent years. They have been reported as the most abundant biological entities on the planet and their ability to impact the composition of bacterial communities is of great interest. In this review, we aim to explore where phages exist in natural and artificial environments and how they impact communities. The natural environment in this review will focus on the human body, soils, and the marine environment. In these naturally occurring environments there is an abundance of phages suggesting a role in the maintenance of bacterial community homeostasis. The artificial environment focuses on wastewater treatment plants, industrial processes, followed by pharmaceutical formulations. As in natural environments, the existence of bacteria in manmade wastewater treatment plants and industrial processes inevitably attracts phages. The presence of phages in these environments can inhibit the bacteria required for efficient water treatment or food production. Alternatively, they can have a positive impact by eliminating recalcitrant organisms. Finally, we conclude by describing how phages can be manipulated or formulated into pharmaceutical products in the laboratory for use in natural or artificial environments.
Collapse
Affiliation(s)
- Steven Batinovic
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Flavia Wassef
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Sarah A Knowler
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Daniel T F Rice
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Cassandra R Stanton
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Jayson Rose
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Joseph Tucci
- Department of Pharmacy & Biomedical Sciences, La Trobe University, Bendigo, VIC 3550, Australia
| | - Tadashi Nittami
- Division of Materials Science and Chemical Engineering, Yokohama National University, Yokohama 240-8501, Japan
| | - Antony Vinh
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Grant R Drummond
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Christopher G Sobey
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Hiu Tat Chan
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Robert J Seviour
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia.
| | - Ashley E Franks
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| |
Collapse
|
21
|
Michniewski S, Redgwell T, Grigonyte A, Rihtman B, Aguilo‐Ferretjans M, Christie‐Oleza J, Jameson E, Scanlan DJ, Millard AD. Riding the wave of genomics to investigate aquatic coliphage diversity and activity. Environ Microbiol 2019; 21:2112-2128. [PMID: 30884081 PMCID: PMC6563131 DOI: 10.1111/1462-2920.14590] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/17/2022]
Abstract
Bacteriophages infecting Escherichia coli (coliphages) have been used as a proxy for faecal matter and water quality from a variety of environments. However, the diversity of coliphages that is present in seawater remains largely unknown, with previous studies largely focusing on morphological diversity. Here, we isolated and characterized coliphages from three coastal locations in the United Kingdom and Poland. Comparative genomics and phylogenetic analysis of phage isolates facilitated the identification of putative new species within the genera Rb69virus and T5virus and a putative new genus within the subfamily Tunavirinae. Furthermore, genomic and proteomic analysis combined with host range analysis allowed the identification of a putative tail fibre that is likely responsible for the observed differences in host range of phages vB_Eco_mar003J3 and vB_Eco_mar004NP2.
Collapse
Affiliation(s)
- Slawomir Michniewski
- School of Life SciencesUniversity of WarwickGibbet Hill Road, Coventry CV4 7ALUK
| | - Tamsin Redgwell
- School of Life SciencesUniversity of WarwickGibbet Hill Road, Coventry CV4 7ALUK
| | - Aurelija Grigonyte
- School of Life SciencesUniversity of WarwickGibbet Hill Road, Coventry CV4 7ALUK
| | - Branko Rihtman
- School of Life SciencesUniversity of WarwickGibbet Hill Road, Coventry CV4 7ALUK
| | | | | | - Eleanor Jameson
- School of Life SciencesUniversity of WarwickGibbet Hill Road, Coventry CV4 7ALUK
| | - David J. Scanlan
- School of Life SciencesUniversity of WarwickGibbet Hill Road, Coventry CV4 7ALUK
| | - Andrew D. Millard
- Department of Genetics and Genome BiologyUniversity of Leicester, University RoadLeicester LE1 7RHUK
| |
Collapse
|
22
|
Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes. Nat Commun 2019; 10:1169. [PMID: 30862830 PMCID: PMC6414667 DOI: 10.1038/s41467-019-09106-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/21/2019] [Indexed: 12/11/2022] Open
Abstract
Viruses provide top-down control on microbial communities, yet their direct study in natural environments was hindered by culture limitations. The advance of bioinformatics enables cultivation-independent study of viruses. Many studies assemble new viral genomes and study viral diversity using marker genes from free viruses. Here we use cellular metatranscriptomics to study active community-wide viral infections. Recruitment to viral contigs allows tracking infection dynamics over time and space. Our assemblies represent viral populations, but appear biased towards low diversity viral taxa. Tracking relatives of published T4-like cyanophages and pelagiphages reveals high genomic continuity. We determine potential hosts by matching dynamics of infection with abundance of particular microbial taxa. Finally, we quantify the relative contribution of cyanobacteria and viruses to photosystem-II psbA (reaction center) expression in our study sites. We show sometimes >50% of all cyanobacterial+viral psbA expression is of viral origin, highlighting the contribution of viruses to photosynthesis and oxygen production. Here, Sieradzki et al. use metatranscriptomics to study active community-wide viral infections at three coastal California sites throughout a year, identify potential viral hosts, and show that viruses can contribute a substantial amount to photosystem-II psbA expression.
Collapse
|
23
|
Castelán-Sánchez HG, Lopéz-Rosas I, García-Suastegui WA, Peralta R, Dobson ADW, Batista-García RA, Dávila-Ramos S. Extremophile deep-sea viral communities from hydrothermal vents: Structural and functional analysis. Mar Genomics 2019; 46:16-28. [PMID: 30857856 DOI: 10.1016/j.margen.2019.03.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/25/2019] [Accepted: 03/01/2019] [Indexed: 12/29/2022]
Abstract
Ten publicly available metagenomic data sets from hydrothermal vents were analyzed to determine the taxonomic structure of the viral communities present, as well as their potential metabolic functions. The type of natural selection on two auxiliary metabolic genes was also analyzed. The structure of the virome in the hydrothermal vents was quite different in comparison with the viruses present in sediments, with specific populations being present in greater abundance in the plume samples when compared with the sediment samples. ssDNA genomes such as Circoviridae and Microviridae were predominantly present in the sediment samples, with Caudovirales which are dsDNA being present in the vent samples. Genes potentially encoding enzymes that participate in carbon, nitrogen and sulfur metabolic pathways were found in greater abundance, than those involved in the oxygen cycle, in the hydrothermal vents. Functional profiling of the viromes, resulted in the discovery of genes encoding proteins involved in bacteriophage capsids, DNA synthesis, nucleotide synthesis, DNA repair, as well as viral auxiliary metabolic genes such as cytitidyltransferase and ribonucleotide reductase. These auxiliary metabolic genes participate in the synthesis of phospholipids and nucleotides respectively and are likely to contribute to enhancing the fitness of their bacterial hosts within the hydrothermal vent communities. Finally, evolutionary analysis suggested that these auxiliary metabolic genes are highly conserved and evolve under purifying selection, and are thus maintained in their genome.
Collapse
Affiliation(s)
- Hugo G Castelán-Sánchez
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa. Cuernavca, Morelos. C.P, Cuernavaca 62209, Mexico
| | - Itzel Lopéz-Rosas
- CONACyT Research fellow-Colegio de Postgraduados Campus Campeche, Carretera Haltunchén - Edzná Km 17.5. Colonia Sihochac. Champotón, Campeche 24450, Mexico
| | - Wendy A García-Suastegui
- Laboratorio de Toxicología Molecular, Departamento de Biología y Toxicología de la Reproducción, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla C.P., 72570, Mexico
| | - Raúl Peralta
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa. Cuernavca, Morelos. C.P, Cuernavaca 62209, Mexico
| | - Alan D W Dobson
- School of Microbiology, University College Cork. Cork, Ireland; Environmental Research Institute, University College, Cork, Ireland
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa. Cuernavca, Morelos. C.P, Cuernavaca 62209, Mexico
| | - Sonia Dávila-Ramos
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa. Cuernavca, Morelos. C.P, Cuernavaca 62209, Mexico.
| |
Collapse
|
24
|
Roux S, Brum JR. A viral reckoning: viruses emerge as essential manipulators of global ecosystems. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:3-8. [PMID: 30298570 DOI: 10.1111/1758-2229.12700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 09/30/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Simon Roux
- US DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, 94598, USA
| | - Jennifer R Brum
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA, 70808, USA
| |
Collapse
|
25
|
Affiliation(s)
- Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- * E-mail:
| |
Collapse
|
26
|
Martin RM, Moniruzzaman M, Mucci NC, Willis A, Woodhouse JN, Xian Y, Xiao C, Brussaard CPD, Wilhelm SW. Cylindrospermopsis raciborskii Virus and host: genomic characterization and ecological relevance. Environ Microbiol 2018; 21:1942-1956. [PMID: 30251319 DOI: 10.1111/1462-2920.14425] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 01/21/2023]
Abstract
Cylindrospermopsis (Raphidiopsis) raciborskii is an invasive, filamentous, nitrogen-fixing cyanobacterium that forms frequent blooms in freshwater habitats. While viruses play key roles in regulating the abundance, production and diversity of their hosts in aquatic ecosystems, the role(s) of viruses in the ecology of C. raciborskii is almost unexplored. Progress in this field has been hindered by the absence of a characterized virus-host system in C. raciborskii. To bridge this gap, we sequenced the genome of CrV-01T, a previously isolated cyanosiphovirus, and its host, C. raciborskii strain Cr2010. Analyses suggest that CrV-01T represents a distinct clade of siphoviruses infecting, and perhaps lysogenizing, filamentous cyanobacteria. Its genome contains unique features that include an intact CRISPR array and a 12 kb inverted duplication. Evidence suggests CrV-01T recently gained the ability to infect Cr2010 and recently lost the ability to form lysogens. The cyanobacterial host contains a CRISPR-Cas system with CRISPR spacers matching protospacers within the inverted duplication of the CrV-01T genome. Examination of metagenomes demonstrates that viruses with high genetic identity to CrV-01T, but lacking the inverted duplication, are present in C. raciborskii blooms in Australia. The unique genomic features of the CrV/Cr2010 system offers opportunities to investigate in more detail virus-host interactions in an ecologically important bloom-forming cyanobacterium.
Collapse
Affiliation(s)
- Robbie M Martin
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | | | - Nicholas C Mucci
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Anusuya Willis
- Australian National Algae Culture Collection, CSIRO National Collections and Marine Infrastructure, Hobart, Australia
| | - Jason N Woodhouse
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Yuejiao Xian
- Department of Chemistry, University of Texas at El Paso, El Paso, TX, USA
| | - Chuan Xiao
- Department of Chemistry, University of Texas at El Paso, El Paso, TX, USA
| | - Corina P D Brussaard
- Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Royal Netherlands Institute for Sea Research, Texel, The Netherlands
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| |
Collapse
|
27
|
Sazinas P, Redgwell T, Rihtman B, Grigonyte A, Michniewski S, Scanlan DJ, Hobman J, Millard A. Comparative Genomics of Bacteriophage of the Genus Seuratvirus. Genome Biol Evol 2018; 10:72-76. [PMID: 29272407 PMCID: PMC5758909 DOI: 10.1093/gbe/evx275] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2017] [Indexed: 01/08/2023] Open
Abstract
Despite being more abundant and having smaller genomes than their bacterial host, relatively few bacteriophages have had their genomes sequenced. Here, we isolated 14 bacteriophages from cattle slurry and performed de novo genome sequencing, assembly, and annotation. The commonly used marker genes polB and terL showed these bacteriophages to be closely related to members of the genus Seuratvirus. We performed a core-gene analysis using the 14 new and four closely related genomes. A total of 58 core genes were identified, the majority of which has no known function. These genes were used to construct a core-gene phylogeny, the results of which confirmed the new isolates to be part of the genus Seuratvirus and expanded the number of species within this genus to four. All bacteriophages within the genus contained the genes queCDE encoding enzymes involved in queuosine biosynthesis. We suggest these genes are carried as a mechanism to modify DNA in order to protect these bacteriophages against host endonucleases.
Collapse
Affiliation(s)
- Pavelas Sazinas
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Tamsin Redgwell
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Branko Rihtman
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | | | | | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Jon Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, United Kingdom
| | - Andrew Millard
- Department of Infection, Immunity and Inflammation, University of Leicester, United Kingdom
| |
Collapse
|
28
|
Zhan Y, Chen F. The smallest ssDNA phage infecting a marine bacterium. Environ Microbiol 2018; 21:1916-1928. [PMID: 30160044 DOI: 10.1111/1462-2920.14394] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 11/28/2022]
Abstract
In the marine environment, only a few lytic single-stranded DNA (ssDNA) phages have been isolated and characterized, despite the fact that diverse ssDNA bacteriophages have been discovered via metagenomic studies. In this study, we isolated and characterized a new ssDNA phage, vB_RpoMi-Mini, which infects a marine bacterium Ruegeria pomeroyi DSS-3. With a genome size of 4248 bp and only four putative open reading frames (ORF), vB_RpoMi-Mini becomes the smallest ssDNA phage among the known ssDNA phage isolates and represents the DNA bacteriophage with the least number of ORFs. Genome-wide analysis reveals that bacteriophage Mini is distantly related to the known ssDNA phages and belongs to an unclassified ssDNA phage within the Microviridae family. The presence of peptidase in vB_RpoMi-Mini genome further implies that horizontal gene transfer could be an important driving force in the evolution of ssDNA phages. Bacteriophage Mini seems to have lost the spike protein commonly seen in ssDNA phages, suggesting that ssDNA phage can be more diverse than previously thought. Metagenomic analysis indicates that Mini-like phages are widely distributed in the environments. The discovery of vB_RpoMi-Mini expands our understanding of ssDNA phages in nature, and also indicates our dearth of knowledge regarding of ssDNA phages.
Collapse
Affiliation(s)
- Yuanchao Zhan
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Cambridge, MD, USA
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Cambridge, MD, USA
| |
Collapse
|
29
|
Kongari R, Rajaure M, Cahill J, Rasche E, Mijalis E, Berry J, Young R. Phage spanins: diversity, topological dynamics and gene convergence. BMC Bioinformatics 2018; 19:326. [PMID: 30219026 PMCID: PMC6139136 DOI: 10.1186/s12859-018-2342-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 08/28/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Spanins are phage lysis proteins required to disrupt the outer membrane. Phages employ either two-component spanins or unimolecular spanins in this final step of Gram-negative host lysis. Two-component spanins like Rz-Rz1 from phage lambda consist of an integral inner membrane protein: i-spanin, and an outer membrane lipoprotein: o-spanin, that form a complex spanning the periplasm. Two-component spanins exist in three different genetic architectures; embedded, overlapped and separated. In contrast, the unimolecular spanins, like gp11 from phage T1, have an N-terminal lipoylation signal sequence and a C-terminal transmembrane domain to account for the topology requirements. Our proposed model for spanin function, for both spanin types, follows a common theme of the outer membrane getting fused with the inner membrane, effecting the release of progeny virions. RESULTS Here we present a SpaninDataBase which consists of 528 two-component spanins and 58 unimolecular spanins identified in this analysis. Primary analysis revealed significant differences in the secondary structure predictions for the periplasmic domains of the two-component and unimolecular spanin types, as well as within the three different genetic architectures of the two-component spanins. Using a threshold of 40% sequence identity over 40% sequence length, we were able to group the spanins into 143 i-spanin, 125 o-spanin and 13 u-spanin families. More than 40% of these families from each type were singletons, underlining the extreme diversity of this class of lysis proteins. Multiple sequence alignments of periplasmic domains demonstrated conserved secondary structure patterns and domain organization within family members. Furthermore, analysis of families with members from different architecture allowed us to interpret the evolutionary dynamics of spanin gene arrangement. Also, the potential universal role of intermolecular disulfide bonds in two-component spanin function was substantiated through bioinformatic and genetic approaches. Additionally, a novel lipobox motif, AWAC, was identified and experimentally verified. CONCLUSIONS The findings from this bioinformatic approach gave us instructive insights into spanin function, evolution, domain organization and provide a platform for future spanin annotation, as well as biochemical and genetic experiments. They also establish that spanins, like viral membrane fusion proteins, adopt different strategies to achieve fusion of the inner and outer membranes.
Collapse
Affiliation(s)
- Rohit Kongari
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843-2128, USA
| | | | - Jesse Cahill
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843-2128, USA
| | - Eric Rasche
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843-2128, USA
| | - Eleni Mijalis
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843-2128, USA
| | - Joel Berry
- University of California, San Francisco, CA, USA
| | - Ry Young
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843-2128, USA.
| |
Collapse
|
30
|
Vater A, Byrne BA, Marshman BC, Ashlock LW, Moore JD. Differing responses of red abalone ( Haliotis rufescens) and white abalone ( H. sorenseni) to infection with phage-associated Candidatus Xenohaliotis californiensis. PeerJ 2018; 6:e5104. [PMID: 29967748 PMCID: PMC6022723 DOI: 10.7717/peerj.5104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/05/2018] [Indexed: 11/20/2022] Open
Abstract
The Rickettsiales-like prokaryote and causative agent of Withering Syndrome (WS)-Candidatus Xenohaliotis californiensis (Ca. Xc)-decimated black abalone populations along the Pacific coast of North America. White abalone-Haliotis sorenseni-are also susceptible to WS and have become nearly extinct in the wild due to overfishing in the 1970s. Candidatus Xenohaliotis californiensis proliferates within epithelial cells of the abalone gastrointestinal tract and causes clinical signs of starvation. In 2012, evidence of a putative bacteriophage associated with Ca. Xc in red abalone-Haliotis rufescens-was described. Recently, histologic examination of animals with Ca. Xc infection in California abalone populations universally appear to have the phage-containing inclusions. In this study, we investigated the current virulence of Ca. Xc in red abalone and white abalone at different environmental temperatures. Using a comparative experimental design, we observed differences over time between the two abalone species in mortality, body condition, and bacterial load by quantitative real time PCR (qPCR). By day 251, all white abalone exposed to the current variant of Ca. Xc held in the warm water (18.5 °C) treatment died, while red abalone exposed to the same conditions had a mortality rate of only 10%, despite a relatively heavy bacterial burden as determined by qPCR of posterior esophagus tissue and histological assessment at the termination of the experiment. These data support the current status of Ca. Xc as less virulent in red abalone, and may provide correlative evidence of a protective phage interaction. However, white abalone appear to remain highly susceptible to this disease. These findings have important implications for implementation of a white abalone recovery program, particularly with respect to the thermal regimes of locations where captively-reared individuals will be outplanted.
Collapse
Affiliation(s)
- Ashley Vater
- Integrative Pathobiology Graduate Group, University of California, Davis, Davis, United States of America
| | - Barbara A. Byrne
- Pathology, Microbiology, Immunology, School of Veterinary Medicine, University of California, Davis, Davis, United States of America
| | - Blythe C. Marshman
- Shellfish Health Laboratory, California Department of Fish and Wildlife, Bodega Bay, United States of America
| | - Lauren W. Ashlock
- Shellfish Health Laboratory, California Department of Fish and Wildlife, Bodega Bay, United States of America
| | - James D. Moore
- Shellfish Health Laboratory, California Department of Fish and Wildlife, Bodega Bay, United States of America
- Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, Davis, United States of America
| |
Collapse
|
31
|
Watkins SC, Sible E, Putonti C. Pseudomonas PB1-Like Phages: Whole Genomes from Metagenomes Offer Insight into an Abundant Group of Bacteriophages. Viruses 2018; 10:v10060331. [PMID: 29914169 PMCID: PMC6024596 DOI: 10.3390/v10060331] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/11/2018] [Accepted: 06/11/2018] [Indexed: 02/07/2023] Open
Abstract
Despite the abundance, ubiquity and impact of environmental viruses, their inherent genomic plasticity and extreme diversity pose significant challenges for the examination of bacteriophages on Earth. Viral metagenomic studies have offered insight into broader aspects of phage ecology and repeatedly uncover genes to which we are currently unable to assign function. A combined effort of phage isolation and metagenomic survey of Chicago’s nearshore waters of Lake Michigan revealed the presence of Pbunaviruses, relatives of the Pseudomonas phage PB1. This prompted our expansive investigation of PB1-like phages. Genomic signatures of PB1-like phages and Pbunaviruses were identified, permitting the unambiguous distinction between the presence/absence of these phages in soils, freshwater and wastewater samples, as well as publicly available viral metagenomic datasets. This bioinformatic analysis led to the de novo assembly of nine novel PB1-like phage genomes from a metagenomic survey of samples collected from Lake Michigan. While this study finds that Pbunaviruses are abundant in various environments of Northern Illinois, genomic variation also exists to a considerable extent within individual communities.
Collapse
Affiliation(s)
- Siobhan C Watkins
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA.
| | - Emily Sible
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA.
| | - Catherine Putonti
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA.
- Department of Computer Science, Loyola University Chicago, Chicago, IL 60660, USA.
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA.
| |
Collapse
|
32
|
Howard-Varona C, Hargreaves KR, Solonenko NE, Markillie LM, White RA, Brewer HM, Ansong C, Orr G, Adkins JN, Sullivan MB. Multiple mechanisms drive phage infection efficiency in nearly identical hosts. THE ISME JOURNAL 2018; 12:1605-1618. [PMID: 29568113 PMCID: PMC5955906 DOI: 10.1038/s41396-018-0099-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 01/08/2018] [Accepted: 02/20/2018] [Indexed: 12/15/2022]
Abstract
Phage-host interactions are critical to ecology, evolution, and biotechnology. Central to those is infection efficiency, which remains poorly understood, particularly in nature. Here we apply genome-wide transcriptomics and proteomics to investigate infection efficiency in nature's own experiment: two nearly identical (genetically and physiologically) Bacteroidetes bacterial strains (host18 and host38) that are genetically intractable, but environmentally important, where phage infection efficiency varies. On host18, specialist phage phi18:3 infects efficiently, whereas generalist phi38:1 infects inefficiently. On host38, only phi38:1 infects, and efficiently. Overall, phi18:3 globally repressed host18's transcriptome and proteome, expressed genes that likely evaded host restriction/modification (R/M) defenses and controlled its metabolism, and synchronized phage transcription with translation. In contrast, phi38:1 failed to repress host18's transcriptome and proteome, did not evade host R/M defenses or express genes for metabolism control, did not synchronize transcripts with proteins and its protein abundances were likely targeted by host proteases. However, on host38, phi38:1 globally repressed host transcriptome and proteome, synchronized phage transcription with translation, and infected host38 efficiently. Together these findings reveal multiple infection inefficiencies. While this contrasts the single mechanisms often revealed in laboratory mutant studies, it likely better reflects the phage-host interaction dynamics that occur in nature.
Collapse
Affiliation(s)
| | | | | | - Lye Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | | | - Heather M Brewer
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | | | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | | | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
33
|
Scola V, Ramond JB, Frossard A, Zablocki O, Adriaenssens EM, Johnson RM, Seely M, Cowan DA. Namib Desert Soil Microbial Community Diversity, Assembly, and Function Along a Natural Xeric Gradient. MICROBIAL ECOLOGY 2018; 75:193-203. [PMID: 28647755 DOI: 10.1007/s00248-017-1009-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/05/2017] [Indexed: 05/25/2023]
Abstract
The hyperarid Namib desert is a coastal desert in southwestern Africa and one of the oldest and driest deserts on the planet. It is characterized by a west/east increasing precipitation gradient and by regular coastal fog events (extending up to 75 km inland) that can also provide soil moisture. In this study, we evaluated the role of this natural aridity and xeric gradient on edaphic microbial community structure and function in the Namib desert. A total of 80 individual soil samples were collected at 10-km intervals along a 190-km transect from the fog-dominated western coastal region to the eastern desert boundary. Seventeen physicochemical parameters were measured for each soil sample. Soil parameters reflected the three a priori defined climatic/xeric zones along the transect ("fog," "low rain," and "high rain"). Microbial community structures were characterized by terminal restriction fragment length polymorphism fingerprinting and shotgun metaviromics, and their functional capacities were determined by extracellular enzyme activity assays. Both microbial community structures and activities differed significantly between the three xeric zones. The deep sequencing of surface soil metavirome libraries also showed shifts in viral composition along the xeric transect. While bacterial community assembly was influenced by soil chemistry and stochasticity along the transect, variations in community "function" were apparently tuned by xeric stress.
Collapse
Affiliation(s)
- Vincent Scola
- Centre for Microbial Ecology and Genomics (CMEG), Department of Microbiology, University of Pretoria, Pretoria, South Africa
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Aline Frossard
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Zürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Olivier Zablocki
- Centre for Microbial Ecology and Genomics (CMEG), Department of Microbiology, University of Pretoria, Pretoria, South Africa
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa
| | - Evelien M Adriaenssens
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Riegardt M Johnson
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Mary Seely
- Gobabeb Research and Training Centre, Walvis Bay, Namibia
- Desert Research Foundation of Namibia (DRFN), Windhoek, Namibia
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa.
| |
Collapse
|
34
|
Culley A. New insight into the RNA aquatic virosphere via viromics. Virus Res 2017; 244:84-89. [PMID: 29138044 DOI: 10.1016/j.virusres.2017.11.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 01/09/2023]
Abstract
RNA viruses that infect microbes are now recognized as an active, persistent and important component of the aquatic microbial community. While some information about the diversity and dynamics of the RNA virioplankton has been derived from culture-based and single gene approaches, research based on viromic and metatransciptomic methods has generated unprecedented insight into this relatively understudied class of microbes. Here, the relevant literature is summarized and discussed, including viromic studies of extracellular aquatic RNA viral assemblages, and transcriptomic studies of active and associated RNA viruses from aquatic environments followed by commentary on the present challenges and future directions of this field of research.
Collapse
Affiliation(s)
- Alexander Culley
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec, Québec, G1V 0A6, Canada; Centre d'études nordiques (CEN), Université Laval, Québec, Québec, G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada; Takuvik, Unité Mixte Interntionale (UMI 3376) Université Laval (Canada) & Centre National de la Recherche Scientifique (France), Québec QC GIV 0A6, Canada.
| |
Collapse
|
35
|
Williamson KE, Fuhrmann JJ, Wommack KE, Radosevich M. Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory. Annu Rev Virol 2017; 4:201-219. [PMID: 28961409 DOI: 10.1146/annurev-virology-101416-041639] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viral abundance in soils can range from below detection limits in hot deserts to over 1 billion per gram in wetlands. Abundance appears to be strongly influenced by water availability and temperature, but a lack of informational standards creates difficulties for cross-study analysis. Soil viral diversity is severely underestimated and undersampled, although current measures of viral richness are higher for soils than for aquatic ecosystems. Both morphometric and metagenomic analyses have raised questions about the prevalence of nontailed, ssDNA viruses in soils. Soil is complex and critically important to terrestrial biodiversity and human civilization, but impacts of viral activities on soil ecosystem services are poorly understood. While information from aquatic systems and medical microbiology suggests the potential for viral influences on nutrient cycles, food web interactions, gene transfer, and other key processes in soils, very few empirical data are available. To understand the soil virome, much work remains.
Collapse
Affiliation(s)
- Kurt E Williamson
- Biology Department, College of William and Mary, Williamsburg, Virginia 23185;
| | - Jeffry J Fuhrmann
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19716
| | - K Eric Wommack
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19716.,Department Biological Sciences, University of Delaware, Newark, Delaware 19716.,College of Earth, Ocean, and Environment, University of Delaware, Newark, Delaware 19716
| | - Mark Radosevich
- Biosystems Engineering and Soil Science Department, University of Tennessee, Knoxville, Tennessee 37996
| |
Collapse
|
36
|
Bacteriophage evolution differs by host, lifestyle and genome. Nat Microbiol 2017; 2:17112. [PMID: 28692019 PMCID: PMC5540316 DOI: 10.1038/nmicrobiol.2017.112] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/09/2017] [Indexed: 01/21/2023]
Abstract
Bacteriophages play key roles in microbial evolution1,2, marine nutrient cycling3 and human disease4. Phages are genetically diverse, and their genome architectures are characteristically mosaic, driven by horizontal gene transfer with other phages and host genomes5. As a consequence, phage evolution is complex and their genomes are composed of genes with distinct and varied evolutionary histories6,7. However, there are conflicting perspectives on the roles of mosaicism and the extent to which it generates a spectrum of genome diversity8 or genetically discrete populations9,10. Here, we show that bacteriophages evolve within two general evolutionary modes that differ in the extent of horizontal gene transfer by an order of magnitude. Temperate phages distribute into high and low gene flux modes, whereas lytic phages share only the lower gene flux mode. The evolutionary modes are also a function of the bacterial host and different proportions of temperate and lytic phages are distributed in either mode depending on the host phylum. Groups of genetically related phages fall into either the high or low gene flux modes, suggesting there are genetic as well as ecological drivers of horizontal gene transfer rates. Consequently, genome mosaicism varies depending on the host, lifestyle and genetic constitution of phages.
Collapse
|
37
|
Affiliation(s)
- Corina P D Brussaard
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute of Sea Research and University of Utrecht, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road, New Brunswick, New Jersey 08901, USA
| | - Carlos Pedrós-Alió
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Catherine Legrand
- Department of Biology and Environmental Science, Center of Ecology and Evolution in Microbial model Systems (EEMiS), Linnæeus University, 39182 Kalmar, Sweden
| |
Collapse
|