Bacteriophages, or phages, have historically been distinguished by their small sizes and relatively simple genomes compared to cellular life. Discoveries over recent decades, however, have uncovered remarkably large phages, called jumbo phages, which are defined by having genomes over 200 kilobases and contain virion sizes comparable to small bacteria. These exceptionally large phages prompt questions on how such complexity emerges and persists in the virosphere, when being simple is so successful with shorter replication times and larger burst sizes. This dissertation aims to address these knowledge gaps by examining the evolutionary and ecological contexts of genomic and community-level complexity of phages using a variety of metagenomic datasets, namely from marine environments. Toward understanding the coexistence of jumbo phages among smaller phages, Chapter 1 provides a literature review on jumbo phage diversity, associated fitness tradeoffs of largeness, and predictions on which environments or ecological conditions may be enriched in jumbo phages. Chapter 2 assesses the evolutionary context giving rise to complex phages, by examining a group of phages that encode a multi-subunit DNA-dependent RNA polymerase homologous to that of cells. This gene fortuitously enabled phylogenetic analyses of phages with cellular life and revealed that these phages likely emerged prior to the divergence of bacteria and archaea, rather than acquiring the gene from their hosts more recently. Chapter 3 examines the biogeography of genomic complexity in the ocean by identifying and comparing groups of jumbo phages in seawater metagenomes of the global ocean. This work revealed that jumbo phages with distinct replication machinery also have distinct distributions, with some groups more common in surface waters than deeper waters and vice versa. Chapter 4 compares drivers of phage complexity at the community level (based on diversity) with the drivers of prokaryotic community diversity by examining seawater metagenomes from contrasting ecosystems off the coasts of the Isthmus of Panama. Despite phages' requiring their hosts to replicate, the results show that factors increasing phage and prokaryotic diversity do not always align. This discrepancy highlights the role the environment also plays in governing virus-host interactions, such as impacting dispersal ranges and adsorption efficiency. Collectively, this dissertation addresses how, what, and where complexity in the virosphere occurs using culture-independent methods and contributes to our growing understanding of the breadth of viral diversity and ecology. / Doctor of Philosophy / While many viruses cause disease and threaten animal and plant health, most viruses on Earth infect microbes, which are tiny, single-celled organisms like bacteria. These viruses can be used to kill harmful bacteria, like certain Escherichia coli (E. coli), and they impact the movement of nutrients in ecosystems because microbes like algae form the basis of food webs in the sea. While most known viruses are very tiny, larger viruses have been recently discovered over recent decades. Being a big virus can be very costly, as it takes more resources for these viruses to replicate or reproduce. Despite these costs, big viruses can be found in many environments around the world, such as the human intestine and the deep sea, which suggests that being large as a virus might be useful in some circumstances. This dissertation aims to uncover how, why, and where being large as a virus is most successful. This research specifically focuses on a group of viruses called phages, which are viruses that infect microbes called bacteria and archaea. Larger phages, those with genomes four times the size of most other phages and twenty times the size of the COVID19 virus, are called jumbo phages. Chapter 1describes the diversity of jumbo phages, what advantages they may have over smaller phages and which environments these advantages may be most helpful. Chapter 2 examines how complex phages evolved by analyzing a group of phages that have a special gene that is also found in all cellular life (microbes, plants, and animals). The evolutionary history of this gene suggests that phages possessed this gene prior to the emergence of major cellular groups (bacteria, archaea, and eukarya), rather than stealing this gene from their host more recently. Chapter 3 uncovers where different types of jumbo phages are most prevalent in the ocean; some are more common in surface waters, and some are more common in deeper waters. Finally, Chapter 4 aims to understand the complexity of phage communities in terms of where phages are most diverse. We found they are more diverse in habitats where bacterial diversity is lower, which is unexpected but shows that the environment plays a major role in virus-host interactions. Overall, this dissertation uncovers the diversity, distribution, and origins of complexity in phages and phage communities, so that we can better understand how they impact the environment and affect microbes that power ecosystems.
| Identifer | oai:union.ndltd.org:VTETD/oai:vtechworks.lib.vt.edu:10919/113829 |
| Date | 14 February 2023 |
| Creators | Weinheimer, Alaina Rose |
| Contributors | Biological Sciences, Aylward, Frank O., Zhang, Liqing, Jensen, Roderick V., Stevens, Ann M. |
| Publisher | Virginia Tech |
| Source Sets | Virginia Tech Theses and Dissertation |
| Language | English |
| Detected Language | English |
| Type | Dissertation |
| Format | ETD, application/pdf, application/pdf |
| Rights | In Copyright, http://rightsstatements.org/vocab/InC/1.0/ |
Page generated in 0.0022 seconds