The Arctic fresh water virome

SpitsbergenAlthough we now understand that viruses are the most abundant organisms on Earth, there are gaps in our knowledge about their distribution in different environments. Results of a new study reveal the diversity and distribution of viruses in Arctic fresh waters.

Fresh waters in high latitudes such as the Arctic and Antarctic have low levels of nutrients (e.g. are oligotrophic) and support the growth mainly of microorganisms. They are good model systems for understanding how viruses affect microbial communities and the entire ecosystem. It is known that diverse viral communities, comprising novel families of single-stranded (ss) DNA viruses, dominate the fresh waters of the Antarctic Lake Limnopolar. However no large scale studies of the Arctic fresh water virome have been done.

Fresh water was collected in three different years from six lakes in Spitsbergen, Norway (red symbol on map). Viral particles were purified from the water samples and their genome sequences were determined. Only about 10% of the viral sequences could be assigned to a previously known virus family. Most (86%) of the recognizable sequences were from ssDNA viruses, and similar viruses were found in all six lakes.

Comparisons with viromes from other freshwater locations revealed similar taxonomic distributions in Antarctic freshwater but not elsewhere. As these locations are at opposite ends of the global poles, the results suggest that some viruses may be dispersed over long distances. The Arctic and Antarctic fresh water viromes do contain different viral species, despite being quite similar environments. On the other hand, the Arctic fresh water virome is very different from the Arctic Ocean virome. The finding of diverse viral communities in Arctic and Antarctic fresh waters indicates that, unlike larger organisms, viral richness might not decrease with distance from the equator.

The authors of this study did not characterize the RNA virome of Arctic fresh water lakes, but they did find sequences of single-stranded RNA viruses in their data sets. Because the authors sequenced DNA only (their protocol did not include a step to convert RNA to DNA before amplification), these RNA viral sequences likely represent DNA-RNA hybrid viruses. These viruses probably were produced by recombination of a DNA virus with DNA produced by reverse transcription of an RNA virus.

When Lake Limnopolar thaws in the spring, its viral community changes from ssDNA viruses to dsDNA viruses, perhaps as the hosts also change. Whether similar changes take place in Spitsbergen should be determined to help illuminate how viruses control high latitude microbial communities.

TWiV 289: Vinny and the capsids

On episode #289 of the science show This Week in VirologyVinny and the capsids answer listener questions about the definition of life, state vaccination laws, the basic science funding problem, viral ecology, inactivation of viruses by pressure, and much more.

You can find TWiV #289 at www.microbe.tv/twiv.

The Vertical Farm

I’ve been hearing about the vertical farm concept from Dickson Despommier for years – as a faculty colleague of his here at Columbia University Medical Center, and more recently as co-host of TWiV and TWiP. I could not help but be enthusiastic as the idea grew from a seed, to seeing Dickson jetting around the globe trying to build the first prototype. Now that the eponymous book is out, does it stand up to the hype?

The Vertical Farm begins with a brief history of agriculture: how humans learned how to grow their food, slowly developing the technology to eke more and more from the earth. We learn about how machinery, petroleum, and fertilizer have impacted farming. But more importantly, Dr. Despommier reveals how farming, while growing more efficient, has slowly destroyed earth’s ecology. The burning of forests to provide farm lands and the resulting increase in global carbon dioxide, and the agricultural runoff that has lead to destruction of coral reefs, to name just two. Along the way we learn just how destructive big cities can be – New York City alone discards 1 billion gallons a day of grey water. These were the most compelling parts of the book, where I learned how good and bad growing food has been.

Next, Dr. Despommier turns to his solution to these problems and more – the vertical farm. He is clearly excited about how growing crops in skyscrapers, with aeroponic technology and extensive recycling, will solve many of the world’s environmental problems as they relate to agriculture. No longer will we have to discard so much precious water; land can be allowed to return to hardwood forests, decreasing carbon dioxide levels in the atmosphere; and perhaps the coral reefs can rebound as we stop dumping fertilizers into the oceans.  These all seem reasonable scenarios. But will they work?

No one knows – not even Dr. Despommier, the consummate optimist, because a vertical farm has not yet been built. The last parts of the book, which deal with the specifics of the vertical farm, are singularly unsatisfying, because there are no details. As Dr. Despommier admits, this is because he is not an architect or engineer. We would like to know exactly how these farms of the future will be built, and their yields and energy costs, but that information cannot yet be provided. I understand all the reasons why – but perhaps Dr. Despommier should have engaged some experts to provide more details. As a result the latter half of the book is unsatisfying because you just can’t wrap your mind around exactly what these farms will be like.

In the end, The Vertical Farm is a dream by a particularly good dreamer. Whether or not those dreams will come true – Dr. Despommier certainly believes they will – is anyone’s guess. I’m rooting for Dickson and the solution to earth’s future food needs, but we’ll know the answer only when a vertical farm – or two – have been built.

Please accept my apologies for this brief foray away from virology – vrr

The abundant and diverse viruses of the seas

earthWhat is the most abundant biological entity in the oceans?

Viruses, of course! The quantity and diversity of viruses in the seas are staggering. Each milliliter of ocean water contains several million virus particles – a global total of 1030 virions! If lined up end to end, they would stretch 200 million light years into space. Viruses constitute 94% of all nucleic-acid containing particles in the sea and are 15 fold more abundant than bacteria and archaea.

Because viruses kill cells, they have a major impact on ocean ecology. About 1023 virus infections occur each second in the oceans; in surface waters they eliminate 20-40% of prokaryotes daily. Viral lysis converts living organisms into particulate matter that becomes carbon dioxide after respiration and photodegradation. Cell killing by viruses also liberates enough iron to supply the needs of phytoplankton, and leads to the production of dimethyl sulphoxide, a gas that influences the climate of the Earth. Because of these activities, marine viruses have a significant impact on global microbial communities and geothermal cycles.

Most of the marine viruses are bacteriophages, but there are also significant numbers that infect eukaryotic phytoplankton, invertebrates, and vertebrates. The best studied viruses are those that infect commercially important species. Novel viruses are frequently discovered; for example, white spot syndrome virus of panaeid shrimp is a member of a new virus family. Viruses of commercially important finfish include herpesviruses, reoviruses, nodaviruses, birnaviruses, and rhabdoviruses. How these viruses are transmitted among marine species is not understood. Many viruses move between marine and fresh waters, posing threats to fishing industries. The rhabdovirus viral hemorrhagic septicemia virus, which causes disease in European farmed trout, has been isolated from 40 marine fish species, from fish farms in Alaska, and from fish in the Great Lakes.

Many ocean viruses cause disease in marine mammals. Phocid distemper virus is a morbillivirus of Arctic phocid seals that has killed thousands of harbor seals in Europe. Similar viruses kill dolphins and other cetaceans. Many other viruses infect marine mammals and even cause disease in humans, including adenoviruses, herpesviruses, parvoviruses, and caliciviruses. The natural reservoirs of most of these viruses are unknown.

Massive sequencing projects have been used to provide information on the diversity of marine viruses. In these studies, seawater is filtered to remove large particles, virions are purified by centrifugation, and nucleic acids are extracted, amplified, and subjected to pyrosequencing. Bioinformatic approaches are used to sift through megabase data sets to identify viral sequences. In one study the viral genomes (‘viromes’) from the Arctic Ocean, the Sargasso Sea, and the coastal waters of British Columbia and the Gulf of Mexico were compared. Over 90% of the sequences were not found in the GenBank collection. There was also little sequence overlap among the samples from the four sites. Similar studies have revealed a rich array of RNA viruses in two different coastal environments; again, most of the sequences were not present in current databases. From the results of these studies it has been estimated that the oceans probably harbor several hundred thousand viral species.

Much more work is required to understand the diversity of marine viruses and their role in the global ecosystem. From the studies done to date, one conclusion is quite clear: the numbers of viruses in the oceans, and their impact on marine life, is far greater than we we ever imagined. And the zoonotic pool may be much larger than we suspected.

Suttle, C. (2007). Marine viruses — major players in the global ecosystem Nature Reviews Microbiology, 5 (10), 801-812 DOI: 10.1038/nrmicro1750

Angly, F., Felts, B., Breitbart, M., Salamon, P., Edwards, R., Carlson, C., Chan, A., Haynes, M., Kelley, S., Liu, H., Mahaffy, J., Mueller, J., Nulton, J., Olson, R., Parsons, R., Rayhawk, S., Suttle, C., & Rohwer, F. (2006). The Marine Viromes of Four Oceanic Regions PLoS Biology, 4 (11) DOI: 10.1371/journal.pbio.0040368

Culley, A., Lang, A.S., & Suttle, C.A. (2006). Metagenomic Analysis of Coastal RNA Virus Communities Science, 312 (5781), 1795-1798 DOI: 10.1126/science.1127404