Publications by category
Journal articles
Buchholz H, Michelsen M, Parsons R, Bates N, Temperton B (In Press). Draft genomes of Pelagimyophage Mosig EXVC030M and Pelagipodophage Lederberg EXVC029P isolated from Devil’s Hole in Bermuda. Microbiology Resource Announcements
Buchholz H, Michelsen M, Temperton B, Bolanos L, Allen M (In Press). Efficient Dilution-to-Extinction isolation of novel virus-host model systems for fastidious heterotrophic bacteria. The ISME Journal: multidisciplinary journal of microbial ecology
Warwick-Dugdale J, Buchholz H, Allen M, Temperton B (In Press). Host-hijacking and Planktonic Piracy: How Phages Command the Microbial High Seas. Virology
Buchholz HH, Bolaños LM, Bell AG, Michelsen ML, Allen MJ, Temperton B (2022). A Novel and Ubiquitous Marine Methylophage Provides Insights into Viral-Host Coevolution and Possible Host-Range Expansion in Streamlined Marine Heterotrophic Bacteria.
Appl Environ Microbiol,
88(7).
Abstract:
A Novel and Ubiquitous Marine Methylophage Provides Insights into Viral-Host Coevolution and Possible Host-Range Expansion in Streamlined Marine Heterotrophic Bacteria.
The methylotrophic OM43 clade are Gammaproteobacteria that comprise some of the smallest free-living cells known and have highly streamlined genomes. OM43 represents an important microbial link between marine primary production and remineralization of carbon back to the atmosphere. Bacteriophages shape microbial communities and are major drivers of mortality and global marine biogeochemistry. Recent cultivation efforts have brought the first viruses infecting members of the OM43 clade into culture. Here, we characterize a novel myophage infecting OM43 called Melnitz. Melnitz was isolated independently from water samples from a subtropical ocean gyre (Sargasso Sea) and temperate coastal (Western English Channel) systems. Metagenomic recruitment from global ocean viromes confirmed that Melnitz is globally ubiquitous, congruent with patterns of host abundance. Bacteria with streamlined genomes such as OM43 and the globally dominant SAR11 clade use riboswitches as an efficient method to regulate metabolism. Melnitz encodes a two-piece tmRNA (ssrA), controlled by a glutamine riboswitch, providing evidence that riboswitch use also occurs for regulation during phage infection of streamlined heterotrophs. Virally encoded tRNAs and ssrA found in Melnitz were phylogenetically more closely related to those found within the alphaproteobacterial SAR11 clade and their associated myophages than those within their gammaproteobacterial hosts. This suggests the possibility of an ancestral host transition event between SAR11 and OM43. Melnitz and a related myophage that infects SAR11 were unable to infect hosts of the SAR11 and OM43, respectively, suggesting host transition rather than a broadening of host range. IMPORTANCE Isolation and cultivation of viruses are the foundations on which the mechanistic understanding of virus-host interactions and parameterization of bioinformatic tools for viral ecology are based. This study isolated and characterized the first myophage known to infect the OM43 clade, expanding our knowledge of this understudied group of microbes. The nearly identical genomes of four strains of Melnitz isolated from different marine provinces and the global abundance estimations from metagenomic data suggest that this viral population is globally ubiquitous. Genome analysis revealed several unusual features in Melnitz and related genomes recovered from viromes, such as a curli operon and virally encoded tmRNA controlled by a glutamine riboswitch, neither of which are found in the host. Further phylogenetic analysis of shared genes indicates that this group of viruses infecting the gammaproteobacterial OM43 shares a recent common ancestor with viruses infecting the abundant alphaproteobacterial SAR11 clade. Host ranges are affected by compatible cell surface receptors, successful circumvention of superinfection exclusion systems, and the presence of required accessory proteins, which typically limits phages to singular narrow groups of closely related bacterial hosts. This study provides intriguing evidence that for streamlined heterotrophic bacteria, virus-host transitioning may not be necessarily restricted to phylogenetically related hosts but is a function of shared physical and biochemical properties of the cell.
Abstract.
Author URL.
Publications by year
In Press
Buchholz H, Michelsen M, Parsons R, Bates N, Temperton B (In Press). Draft genomes of Pelagimyophage Mosig EXVC030M and Pelagipodophage Lederberg EXVC029P isolated from Devil’s Hole in Bermuda. Microbiology Resource Announcements
Buchholz H, Michelsen M, Temperton B, Bolanos L, Allen M (In Press). Efficient Dilution-to-Extinction isolation of novel virus-host model systems for fastidious heterotrophic bacteria. The ISME Journal: multidisciplinary journal of microbial ecology
Warwick-Dugdale J, Buchholz H, Allen M, Temperton B (In Press). Host-hijacking and Planktonic Piracy: How Phages Command the Microbial High Seas. Virology
2022
Buchholz HH, Bolaños LM, Bell AG, Michelsen ML, Allen MJ, Temperton B (2022). A Novel and Ubiquitous Marine Methylophage Provides Insights into Viral-Host Coevolution and Possible Host-Range Expansion in Streamlined Marine Heterotrophic Bacteria.
Appl Environ Microbiol,
88(7).
Abstract:
A Novel and Ubiquitous Marine Methylophage Provides Insights into Viral-Host Coevolution and Possible Host-Range Expansion in Streamlined Marine Heterotrophic Bacteria.
The methylotrophic OM43 clade are Gammaproteobacteria that comprise some of the smallest free-living cells known and have highly streamlined genomes. OM43 represents an important microbial link between marine primary production and remineralization of carbon back to the atmosphere. Bacteriophages shape microbial communities and are major drivers of mortality and global marine biogeochemistry. Recent cultivation efforts have brought the first viruses infecting members of the OM43 clade into culture. Here, we characterize a novel myophage infecting OM43 called Melnitz. Melnitz was isolated independently from water samples from a subtropical ocean gyre (Sargasso Sea) and temperate coastal (Western English Channel) systems. Metagenomic recruitment from global ocean viromes confirmed that Melnitz is globally ubiquitous, congruent with patterns of host abundance. Bacteria with streamlined genomes such as OM43 and the globally dominant SAR11 clade use riboswitches as an efficient method to regulate metabolism. Melnitz encodes a two-piece tmRNA (ssrA), controlled by a glutamine riboswitch, providing evidence that riboswitch use also occurs for regulation during phage infection of streamlined heterotrophs. Virally encoded tRNAs and ssrA found in Melnitz were phylogenetically more closely related to those found within the alphaproteobacterial SAR11 clade and their associated myophages than those within their gammaproteobacterial hosts. This suggests the possibility of an ancestral host transition event between SAR11 and OM43. Melnitz and a related myophage that infects SAR11 were unable to infect hosts of the SAR11 and OM43, respectively, suggesting host transition rather than a broadening of host range. IMPORTANCE Isolation and cultivation of viruses are the foundations on which the mechanistic understanding of virus-host interactions and parameterization of bioinformatic tools for viral ecology are based. This study isolated and characterized the first myophage known to infect the OM43 clade, expanding our knowledge of this understudied group of microbes. The nearly identical genomes of four strains of Melnitz isolated from different marine provinces and the global abundance estimations from metagenomic data suggest that this viral population is globally ubiquitous. Genome analysis revealed several unusual features in Melnitz and related genomes recovered from viromes, such as a curli operon and virally encoded tmRNA controlled by a glutamine riboswitch, neither of which are found in the host. Further phylogenetic analysis of shared genes indicates that this group of viruses infecting the gammaproteobacterial OM43 shares a recent common ancestor with viruses infecting the abundant alphaproteobacterial SAR11 clade. Host ranges are affected by compatible cell surface receptors, successful circumvention of superinfection exclusion systems, and the presence of required accessory proteins, which typically limits phages to singular narrow groups of closely related bacterial hosts. This study provides intriguing evidence that for streamlined heterotrophic bacteria, virus-host transitioning may not be necessarily restricted to phylogenetically related hosts but is a function of shared physical and biochemical properties of the cell.
Abstract.
Author URL.
Buchholz H (2022). High-throughput isolation and ecogenomics of phages infecting fastidious marine heterotrophic bacteria.
Abstract:
High-throughput isolation and ecogenomics of phages infecting fastidious marine heterotrophic bacteria
Marine Bacteria and their associated viruses are key players in shaping microbial community structures and global biogeochemical cycles. Cell lysis through viral predation is a crucial component for the recycling of carbon compounds and other nutrients, and interaction between viruses and hosts can also alter cellular functions via metabolic ‘hijacking’. The culture-based study of phototrophic cyanobacterial virus-host systems has revealed that these constant co29 evolutionary pressures in virus-host systems are further escalated by virally mediate horizontal gene transfer. Viruses of fastidious, heterotrophic bacteria are among the most abundant and ecologically significant virus-host systems in the oceans, but the dearth of cultured model systems has hampered the progression in testing hypotheses and interpretation of meta’omics data. The central goal of this thesis was to establish efficient and high-throughput methodologies for viral isolation, specifically targeting fastidious heterotrophic microbes. Using a novel isolate of the ubiquitous SAR11 clade as a model for highly abundant hosts, and three novel isolates of the methylotrophic OM43 clade for a lower-abundance host, I devised an optimised workflow based on established Dilution-to-Extinction culturing techniques that resulted in the isolation of over 117 viruses. The results show that among these novel viruses were the first known siphoviruses of the SAR11 clade and the first recorded viruses infecting members of the OM43 clade. Genomic evidence by the Methylophilales phage Melnitz indicated that inter-class host transitioning between streamlined heterotrophs may occur, and highlighted unusual viral features such as curli genes and glutamine riboswitches. Furthermore, utilising the power of metagenomics coupled with culture based host range experiments, the Pelagibacter phage Skadi was revealed as a highly abundant polar virus, and as an example for ecotypic niche specificity among the most abundant viruses on Earth. Culture-based identification of virus-host pairs combined with ecogenomic interpretation of metagenomic data will improve our understanding of ecological patterns and of viral strategies. The results from this thesis illuminated parts of the viral “dark matter” and highlighted possible novel viral strategies. This work can be adapted to many different systems, both of high and low abundance, and should be used to improve future viral isolation campaigns.
Abstract.
