Friday, 24 June 2016 13:04

Bacteriophage: A Drop in the Carbon Ocean

Written by 
Published in Microbial Sciences

Marine Phage - Fig 1
Figure 1. Electron micrograph of negative-stained marine phage—Prochlorococcus myoviruses. Source

The recently announced Microbiome Initiative was warmly received by the ASM (as discussed by Julie Wolf in "Dispatches from ASM Microbe: Sunday"). One aim of the Initiative is that all microbiomes, not just those of humans, should be investigated and understood.

Recent advances in sequencing and culturing technology have made it possible to identify the types of bacteria, archaea, fungi, and parasites present in complex communities. Perturbing these ecosystems in controlled ways teases out data about how members of the community interact with each other and, in turn, what impact they may have on their environment.

One group of microbes, however, has been more difficult to both quantify and identify.


The virome is an ubiquitous component of the microbiome, but using sequence technology to track viruses is challenging in part because they lack pan-species barcode-like regions—such as the rRNA sequences of bacteria, archaea and eukarya. Additionally, the rate of horizontal gene transfer between viruses is astounding, resulting in highly fluid genomes that better resemble the tangrams than jigsaw puzzles.

Tackling this gap in our knowledge has become a priority for some researchers highlighted at the ASM Microbe 2016 meeting in Boston, MA. The Friday afternoon session entitled "Friends, Foes and Frenemies: Phage-Host Dynamics" featured some tantalizing discussions of potential roles for bacteriophage in areas impacting human health, one of them being climate change.

As a group of viruses that literally prey on bacteria and archaea, bacteriophage fill a predatory role in their native ecosystems. Predators help keep prey populations in check, in turn preventing exhaustion of available resources. In addition to prey control, phage are instrumental in the genetic and metabolic diversity of their prey by transduction and alteration of biochemistry during the infection process, respectively.

Jennifer Brum, a research scientist at Ohio State University, has focused her research on the role of phage in ocean microbiomes. Since viruses outnumber bacteria in the ocean 10 to 1, with an estimated 1,023 phage infections occurring per second, she began by asking about phage diversity.

The schooner TARA - Fig 2-2
Figure 2. A Tara Arctic expedition schooner. Source

By sequencing viruses present in samples from Tara Ocean Project stations across the globe, Brum noted more than 5,400 distinct viral populations. While the viral diversity was similar across samples and locations (excepting near the Antarctic), there were particular species that dominated in different environments according to temperature. She hypothesized, with some correlative data ($), that local diversity developed by drawing from the global diversity dispersed by ocean currents. The current knowledge about phage diversity, however, is restricted primarily to dsDNA phage, due to bias and limitations in current sequencing pipelines and technology.

Identifying the diversity of phage populations is only the beginning. Anywhere from 65 to 93% of the genes sequenced are considered viral "dark matter," since their roles are functionally unknown. And fewer than 1% of identified phages are linked taxonomically to bacterial hosts.

Brum outlines several interesting techniques to tackle these gaps in her recent review ($). One uses the prediction of open reading frames (ORFs) as a metric for viral diversity and to reveal the genetic potential of these viruses. By sorting ORFs into protein clusters, or PCs, upwards of 500,000 distinct PCs have been identified. Those present in each of their samples were classified as "core PCs," which are highly enriched in photic zones, upper regions of the ocean that sunlight can reach. By comparison, the number of core PCs detected decreases along with the depth of the ocean. Brum hypothesized that this decrease is due to the sinking of viral particles from the photic zones to the ocean floor.

And this is where climate change comes in.

The recycling of cellular components—like amino acids, nucleic acids, and micronutrients—has been linked to the lysis of bacteria by phage ($). In most environments, this likely forms a closed loop where actively growing bacteria use resources scavenged from the dead. The aggregation of lysed cells, however, may result in large particles that sink in the ocean, contributing to the presence of core PCs in aphotic zones.

This same sedimentation carries the organic matter away from microbes in the photic zones, forcing increased use of atmospheric CO2 to generate more biomass. This idea of carbon export by sedimentation of microbes was proposed as early as 1995, but Brum is one of the first to suggest that phage play a key role in the process.

Her data go on to identify specific viral populations that correlate with, and attempts to connect particular metabolic activities to, increased drawdown of CO2 in the ocean.

Brum hopes that her research can help "inform climate modelling of the global carbon cycle" by creating a framework to include more of the biology that impacts this and other "key ecological processes." The inclusion, and increased funding, of non-human microbiome research in the Microbiome Initiative should also contribute to such ecological models, particularly if other researchers follow Brum’s lead—investigating the contribution of phage to each microbiome.

Last modified on Wednesday, 28 September 2016 15:46
Ada Hagan

Ada Hagan is a graduate student in the Department of Microbiology and Immunology at the University of Michigan. Her doctoral research focuses on the methods that the bacterial pathogen Bacillus anthracis uses to gather iron during infections. Ada is also an advocate for science communication by scientists. She is a co-founder and editor-in-chief of the graduate student science writing blog and a founding member of the Microbial Sciences blog. You can find more on her projects on LinkedIn and by following her on Twitter.