Forest Rohwer

In 2002, as a research scientist San Diego State University, Rohwer performed the first shotgun metagenome (Breitbart et al. 2002). This method of randomly sequencing DNA from the environment transformed the study of viruses and microbes in the environment and associated with macroorganisms.

The first shotgun metagenome, also called virome, showed that there were thousands of viral species per liter of seawater (Breitbart et al. 2002; Angly et al. 2006). Working with Anca Segall, Mya Brietbart, Rob Edwards, and the SDSU Biomath Group, Rohwer performed the first virome studies of corals, soils, sediments and humans (Breitbart et al. 2003, 2005, 2008). Based on this work, he proposed that viruses, and particularly bacteriophage, are the most diverse biological entities on Earth.

Virome studies showed that most viral diversity was extreme and almost completely unknown. Rob Edwards and Rohwer proposed that a genome-based taxonomy was need to link the metagenomic data to the existing, morphology-based taxonomy. The controversial Phage Proteomic Tree was the resulting system and was featured in Life in Our Phage World (2015).

Working with Nancy Knowlton at the Scripps Institution of Oceanography, Rohwer showed that reef-building corals harbored hundreds of thousands of unique bacterial species (Rohwer et al. 2002). They proposed that these bacteria, viruses and other microbes were important for coral health and formed an ecological unit called the holobiont. Further, they hypothesized that changing membership of the holobiont was the primary mechanism of adaption to changing environmental conditions.

In 2005, Rohwer participated in the Northern Line Island expedition headed by Enric Sala and Stuart Sandin. The goal of this research cruise was to determine the effects of human populations on coral reefs. Rohwer performed the first shotgun metagenomes from these islands and proposed that overfishing by humans led to microbialization. Subsequent studies showed microbialization is a global phenomenon and a primary reason for the decline of coral reefs (McDole et al. 2012). This work was featured in Rohwer's book Coral Reef in the Microbial Seas.

While studying corals, Kristen Marhaver and Rohwer noted that bacteriophage, viruses that infect bacteria, were four to five times more abundant than the surrounding seawater. Building on this observation, Jeremy Barr and Rohwer (Barr et al. 2013; 2015) showed that bacteriophage bind to mucus through hypervariable protein domains displayed on the capsid. This effectively concentrates the bacteriophage in the mucus, where they kill bacteria and protect the underlying animal tissue. Rohwer has proposed that this Bacteriophage Attachment to Mucus (BAM) Immunity is the first example and origin of the specific immune response.

Microbialized coral reefs have relatively high bacteria abundances and reduced bacteriophage abundances. To explain this observation, Rohwer and colleagues (Knowles et al. 2016) proposed that the temperate life cycle was the predominant bacteriophage life cycle at high host abundances. The resulting bacterial lysogens would be protected from other bacteriophage via superinfection exclusion and protists via expression of virulence factors.