World’s First Known Virophage – An Intriguing Discovery

Anish Pyne, Indian Institute of Technology, Kharagpur

Very recently, two types of unicellular nano-eukaryotes (protists) were found drifting along the waters of the Gulf of Maine off the North American coast. The organisms depicted certain features that could potentially lead them to be regarded as the world’s first known virophage to science!

INTRODUCTION:

Famous Hungarian-American psychiatrist Thomas Szasz once said, “In the animal kingdom, the rule is, eat or be eaten!” This is the inevitable edict of Mother Nature which drives our complex biosphere and keeps it rolling by connecting every single organism present in every corner of this system, from a single bacterial cell to the largest living animal in the world– the Antarctic Blue Whale. And covering all possible producers, consumers, detritivores, and scavengers. The only exception from this sprawling food web is the Viruses, which can neither be classified as living organisms nor as non-living organisms. Their description even fails to align with the definition of ‘Cells’, hence are referred to as ‘Particles’.

Considering the seemingly almighty disposition of viruses, especially ones that are responsible for the ongoing menace occurring across the globe, the very thought that another organism could potentially be preying on it, one that could feed on viruses, is itself a highly fascinating yet scary idea! Recently scientists in East Boothbay, ME, United States have reported the discovery of certain organisms that can prove the aforementioned idea to be very real. Therefore, the question arises, are we about to witness the world’s first known Virophage. Let’s dive in deeper to find out!

THE DRIVE FOR THE STUDY:

Given the fact that the amount of viral biomass occupying all the terrains, drifting through the atmosphere, and floating through the oceans and other water bodies could easily sum up to constitute the hundreds of tonnes of carbon, phosphorus, and nitrogen that is there in nature, it is rather surprising that other organisms lack mechanisms to directly target these viruses as a sustainable source of resources. To date, there have been only some shreds of evidence of viruses feeding off of other viruses. One example is that of the Mimivirus-dependent virus Sputnik, which is a virophage. But otherwise, evidence of an organism that eats viruses to generate energy to continue its life processes has not been discovered or documented.

Marine planktonic protists are an evolutionarily and functionally diverse group of unicellular eukaryotes which are historically known to prey on huge bacterial populations that are found floating in the oceans. Owing to the immense diversity in phagotrophic protists, resistance to their proliferation, specific predator-prey interactions, and their impact on the biogeochemical cycles remain poorly understood, hence becoming one of the most sought-after research topics today in the domain of marine biology. A research group headed by scientist Julia Brown from the Bigelow Laboratory for Ocean Sciences took interest in these planktonic species and employed single-cell genomic analysis to elucidate the lineage-specific grazing preferences of aplastidic protists in the Gulf of Maine (GoM).

METHODS APPLIED IN THE STUDY:

For this, individual cells were isolated using fluorescence-activated cell sorting (FACS), their genomic DNA was amplified, and the obtained single amplified genomes (SAGs) were PCR-screened for bacterial and eukaryotic rRNA sequences. All these steps were meticulously carried out for 1,698 sample isolates collected from both the Gulf of Marine and the Mediterranean Sea. The GoM samples were collected in Boothbay Harbour, ME, the United States on 19 July 2009, whereas the Mediterranean water samples were collected in 2016 at the BBMO in winter (19 January 2016) and summer (5 July 2016). Both sets of samples were cryopreserved with 6% glycine betaine after initial processing and hence were kept viable for further studies. For detection of bacterial and viral sequences in protistan SAGs, contiguous sequences from eukaryotic SAGs were compared to a collection of bacterial SAGs using MASH software where contiguous sequences originating in protists were considered bacterial if they matched a contiguous sequence from a bacterial SAG at a MASH distance of </= 0.05. Apart from these, ORFs were identified as viral if a putatively viral gene was within the top 10 BLASTn hits when compared to NCBI’s database using MICA-accelerated BLASTn. Virus sequences found in multiple eukaryotic phyla were further characterized via manual examination.

RESULTS AND INFERENCES:

When these samples were further analyzed, around 50% of the libraries from the Mediterranean sample contained bacterial signature sequences which were quite usual owing to the feeding routine of these protists, whereas about 20% of the libraries analyzed from the Gulf of Marine contained the same. Viral sequences on the other hand were somewhat more common in the gulf sample as 50% of the libraries contained fragments of genes from 50 or more different viruses. In the Mediterranean samples, the number for the same was close to 33%.  This was not a surprise in itself as most of the viral signature sequences found were attributed to those of bacteriophages (viruses that infect and replicate inside bacterial cells). So, the presence of viral sequences could be owed to the fact that the bacterial cells which these protists fed on were already pre-infected with the bacteriophages.  But despite this rather simple statistical data, something else came up which was rather unusual! There were particularly two diverse groups of protists, known as Choanozoans and Picozoans, both of which were present in the samples from both the source of water bodies.

Primarily what struck the research group the most was the fact that in multiple samples, there was a complete lack of bacterial DNA, which in turn made the occurrence of viral DNA questionable, as, without proper signs of a bacterial diet, it’s hard to predict how bacteriophage genes could’ve ended up inside the planktons’ cells, without simply concluding this as evidence of a possible viral diet for these protists. Secondly, what was even more compelling was the fact that two completely different phyla of protozoans (Choanozoans and Picozoans) seemed to share almost identical viral sequences, making it even harder to argue that bacteriophage infection was responsible for the presence of viral DNA. Based on these observations, Dr. Brown and her team argued in favor of the evidence, suggesting that the protists potentially had a viral diet. Dr. Brown said further, “Viruses are rich in phosphorus and nitrogen, and could potentially be a good supplement to a carbon-rich diet that might include cellular prey or carbon-rich marine colloids”.

Given the fact that both Choanozoans and Picozoans are present all around the world and are therefore often called “Cosmopolitan Marine Protists”, poses as solid evidence in suggesting that a bacteriophage diet can influence the way we model the flow of nutrients and energy in the marine ecosystem. This is primarily because of a phenomenon known as the “Viral Shunt” which could now be used to contest the existing laws governing the food chain. One of such laws being Lindeman’s “Ten-Percent Law”, according to which ten percent of energy from the nutrients consumed and contained within the bacteria and protozoans are expected to progress upwards through the food chain, as tiny things get eaten by bigger ones and so on. The “Viral Shunt” poses an anomaly to this phenomenon as the virus (bacteriophage) infected bacterial cells get ruptured before they’re being eaten by planktons, which results in the downflow of organic matter or nutrients. As one reaches deeper down the dark and cold depths of the bottomless oceans, the Viral Shunt phenomenon becomes significantly more prominent, with more and more viruses greedily churning through prokaryotes, preventing the birth of diverse food webs. But now knowing that the tables have turned, and prokaryotes seem to have evolved their ways and are biting back by adopting a viral diet. Since this is only the inception of such a remarkable yet peculiar phenomenon depicted by a particular species, more such studies that describe and break down how these processes take place, and could potentially eventually eradicate the very phenomenon of Viral Shunt, are necessary.

“The removal of viruses from the water may reduce the number of viruses available to infect other organisms, while also shuttling the organic carbon within virus particles higher up the food chain,” -Brown, 2020.

Hence, it is safe to assume that we will certainly be more familiar in the upcoming times and have a better understanding of the biology behind the world’s first known virophage.

Also read: Sequence-Scope technology: Imaging without a microscope

References:

1. Brown JM, Labonté JM, Brown J, Record NR, Poulton NJ, Sieracki ME, Logares R and Stepanauskas R (2020) Single Cell Genomics Reveals Viruses Consumed by Marine Protists. Front. Microbiol. 11:524828. DOI: https://doi.org/10.3389/fmicb.2020.524828
2. Choanozoan and picozoan marine protists are probably virus eaters – study. (2020, September 24). Science & Research News | Frontiers. https://blog.frontiersin.org/2020/09/24/choanozoan-and-picozoan-marine-protists-are-probably-virus-eaters-study/

NOTE: The image used is in the public domain in the United States because it was solely created by NASA. NASA copyright policy states that “NASA material is not protected by copyright unless noted“. (See Template:PD-USGov, NASA copyright policy page or JPL Image Use Policy.)

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