Phycodnaviruses: A peek at genetic diversity

Dunigan, David D.; Fitzgerald, Lisa A.; Etten, James L. Van

doi:10.1016/j.virusres.2006.01.024

Cited by 154 publications

(133 citation statements)

References 117 publications

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“…Viral metagenomics has not only confirmed what was previously known about viruses, but it also shed new light on topics such as geographical patterns (Angly et al, 2006;De Corte et al, 2016), and the relationship between their diversity and abundance with biotic and abiotic variables (Breitbart et al, 2004;Dunigan et al, 2006). Recent works have definitely confirmed the early views on viruses as fundamental drivers of many ecosystem processes (Hurwitz and Sullivan, 2013;Malits et al, 2014), and even manipulators of the marine environments (Rohwer and Thurber, 2009).…”

Section: Introductionmentioning

confidence: 67%

“…In a way, the extensive knowledge gathered over the last two decades on the role and importance of viruses in aquatic systems, clearly expressed in exhaustive reviews (e.g., Proctor, 1997;Fuhrman, 1999;Wommack and Colwell, 2000;Weinbauer, 2004;Suttle, 2005;Dunigan et al, 2006;Brum and Sullivan, 2015), has not been followed by its inclusion into marine biogeochemical models. This paper reviews some early knowledge on the activity of viruses and the follow-up (or lack of it) by the modeling community.…”

Section: Introductionmentioning

confidence: 99%

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Bridging the Gap between Knowing and Modeling Viruses in Marine Systems—An Upcoming Frontier

Mateus

2017

Front. Mar. Sci.

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Viruses are the most abundant biological entities in the world's oceans. Their potential control on the dynamics and diversity of bacterioplankton and some phytoplankton groups, and consequent effect on the flow of energy and matter in food webs, may be argued as beyond dispute. Paradoxically, their importance seems to be persistently underestimated by marine modelers, frequently by exclusion, despite the uninterrupted volume of knowledge advanced during the past decades. Bridging the gap between knowing and modeling the role of viruses is, undoubtedly, one of the upcoming frontiers to be crossed in modeling the plankton. This paper has a two-fold objective: (1) review the knowledge on the roles of viruses in marine systems that has been put forward over the past decades, and (2) see how viruses have been incorporated into marine ecosystem models, along with the factors that are limiting their inclusion.

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Section: Introductionmentioning

confidence: 67%

Section: Introductionmentioning

confidence: 99%

Bridging the Gap between Knowing and Modeling Viruses in Marine Systems—An Upcoming Frontier

Mateus

2017

Front. Mar. Sci.

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“…These biological interactions constitute the part of the environment which is most susceptible to rapid change, and their change would create differences in otherwise chemically and physically identical environments and narrow the range of seemingly free-living microbes. Only autotrophic organisms can be considered energetically autonomous, but even microscopic algae have their zooplankton predators (McCauley & Murdoch 1990) and parasites, among them viruses (Dunigan et al 2006) and fungi (e.g. Polyphagus species; Sparrow 1960, p. 449), whose presence would influence the distribution of each species.…”

Section: Introduction In a Series Of Publications Bland Finlay And Thomasmentioning

confidence: 99%

Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi

Taylor

Turner

Townsend

et al. 2006

Phil. Trans. R. Soc. B

304

249

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The claim that eukaryotic micro-organisms have global geographic ranges, constituting a significant departure from the situation with macro-organisms, has been supported by studies of morphological species from protistan kingdoms. Here, we examine this claim by reviewing examples from another kingdom of eukaryotic microbes, the Fungi. We show that inferred geographic range of a fungal species depends upon the method of species recognition. While some fungal species defined by morphology show global geographic ranges, when fungal species are defined by phylogenetic species recognition they are typically shown to harbour several to many endemic species. We advance two non-exclusive reasons to explain the perceived difference between the size of geographic ranges of microscopic and macroscopic eukaryotic species when morphological methods of species recognition are used. These reasons are that microbial organisms generally have fewer morphological characters, and that the rate of morphological change will be slower for organisms with less elaborate development and fewer cells. Both of these reasons result in fewer discriminatory morphological differences between recently diverged lineages. The rate of genetic change, moreover, is similar for both large and small organisms, which helps to explain why phylogenetic species of large and small organisms show a more similar distribution of geographic ranges. As a consequence of the different rates in fungi of genetic and morphological changes, genetic isolation precedes a recognizable morphological change. The final step in speciation, reproductive isolation, also follows genetic isolation and may precede morphological change.

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“…Although phytoplankton viruses are diverse in capsid size, and genome size and type, most cultivated algal viruses belong to the family Phycodnaviridae. Phycodnaviruses are nucleo-cytoplasmic large DNA viruses with capsid sizes ranging from 100-220 nm, and genomes ranging in length from 170 to 560 kb (Van Etten and Meints, 1999;Van Etten et al, 2002;Dunigan et al, 2006). The earliest effort to characterize phycodnavirus communities while circumventing difficulties associated with virus cultivation involved designing algal-virus specific (AVS) PCR primers that targeted DNA polymerase (polB) genes .…”

Section: Introductionmentioning

confidence: 99%

Quantification of virus genes provides evidence for seed-bank populations of phycodnaviruses in Lake Ontario, Canada

2010

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Using quantitative PCR, the abundances of six phytoplankton viruses DNA polymerase (polB) gene fragments were estimated in water samples collected from Lake Ontario, Canada over 26 months. Four of the polB fragments were most related to marine prasinoviruses, while the other two were most closely related to cultivated chloroviruses. Two Prasinovirus-related genes reached peak abundances of 41000 copies ml À1 and were considered 'high abundance', whereas the other two Prasinovirus-related genes peaked at abundances o1000 copies ml À1 and were considered 'low abundance'. Of the genes related to chloroviruses, one peaked at ca 1600 copies ml À1 , whereas the other reached only ca 300 copies ml À1 . Despite these differences in peak abundance, the abundances of all genes monitored were lowest during the late fall, winter and early spring; during these months the high abundance genes persisted at 100-1000 copies ml À1 while the low abundance Prasinovirus-and Chlorovirus-related genes persisted at fewer than ca 100 copies ml À1 . Clone libraries of psbA genes from Lake Ontario revealed numerous Chlorella-like algae and two prasinophytes demonstrating the presence of candidate hosts for all types of viruses monitored. Our results corroborate recent metagenomic analyses that suggest that aquatic virus communities are composed of only a few abundant populations and many low abundance populations. Thus, we speculate that an ecologically important characteristic of phycodnavirus communities is seed-bank populations with members that can become numerically dominant when their host abundances reach appropriate levels.

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Phycodnaviruses: A peek at genetic diversity

Cited by 154 publications

References 117 publications

Bridging the Gap between Knowing and Modeling Viruses in Marine Systems—An Upcoming Frontier

Bridging the Gap between Knowing and Modeling Viruses in Marine Systems—An Upcoming Frontier

Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi

Quantification of virus genes provides evidence for seed-bank populations of phycodnaviruses in Lake Ontario, Canada

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