Novel N4 Bacteriophages Prevail in the Cold Biosphere

Abstract

bColiphage N4 is a lytic bacteriophage discovered nearly half a century ago, and it was considered to be a "genetic orphan" until very recently, when several additional N4-like phages were discovered to infect nonenteric bacterial hosts. Interest in this genus of phages is stimulated by their unique genetic features and propagation strategies. To better understand the ecology of N4-like phages, we investigated the diversity and geographic patterns of N4-like phages by examining 56 Chesapeake Bay viral communities, using a PCR-clone library approach targeting a diagnostic N4-like DNA polymerase gene. Many new lineages of N4-like phages were found in the bay, and their genotypes shift from the lower to the upper bay. Interestingly, signature sequences of N4-like phages were recovered only from winter month samples, when water temperatures were below 4°C. An analysis of existing metagenomic libraries from various aquatic environments supports the hypothesis that N4-like phages are most prolific in colder waters. In particular, a high number of N4-like phages were detected in Organic Lake, Antarctica, a cold and hypersaline system. The prevalence of N4-like phages in the cold biosphere suggests these viruses possess yet-to-be-determined mechanisms that facilitate lytic infections under cold conditions. A s the most abundant microbial form, viruses play important roles in shaping host population structures, mediating genetic exchange between hosts, and modulating trophic transfer in marine food webs (1-3). Marine viral metagenomic studies suggest that viruses encompass the largest genetic repertoire in the ocean (4, 5), yet the functions of ϳ70% of the putative genes identified in viral metagenomic studies remain unknown (6). Recently, several novel phages infecting dominant marine bacteria have been isolated from the ocean (7,8). Both cultivation techniques and molecular approaches suggest that a great many marine viruses await discovery.Bacteriophage N4 was first isolated from sewer waters using Escherichia coli as a host nearly half a century ago (9) and remained a "genetic orphan" for decades, as no other genetically similar phages were characterized. Phage N4 has several unique features with regard to its morphology, physiology, and genome that have made it a focus of study. It has a 70-nm isocahedral capsid, and its genome size is 70 kb. More remarkably, N4 is the only known phage that does not rely on host RNA polymerase for early transcription (10, 11). Instead, it contains a DNA-dependent virionencapsidated RNA polymerase (vRNAP), which is coinjected with viral DNA into its host and initiates transcription (12). The phage also exhibits a lysis-inhibited infection cycle and an extremely large burst size (ca. 3,000 phages per cell), suggestive of a novel mechanism of cell lysis regulation (13,14).The recent renewed interest in the ecology of N4 was prompted by the isolation from a coastal estuary of two new N4-like phages, which infect bacteria of the marine Roseobacter lineage (15). Roseobacters are a widely ...

Bacteriophage Procurement for Therapeutic Purposes

“…Bacteriophages are viruses which have the ability to multiply only in bacterial cells, and they are detectable almost everywhere where live bacteria exist (they have been isolated from all environments and ecological niches, e.g., inland waters, hot springs, salt water, soil, cold water) ( Lin et al, 2010 ; Zheng et al, 2013 ; Zhan et al, 2015 ). It is estimated that in the biosphere there are approximately 10 30-31 phages ( Hendrix et al, 1999 ; Hendrix, 2002 ), which is 10-fold higher than the total number of bacterial cells ( Abedon et al, 2011a ).…”

Bacteriophages that infect marine roseobacters: genomics and ecology

“…Using a pair of group‐specific primers based on the DNA polymerase gene, N4‐like phages were detected in natural samples. N4‐like phages are highly diverse and prevalent in the winter Chesapeake Bay (Zhan et al ., ). A global survey on their distribution indicated that N4‐like phages appear to be restricted to the high latitude marine environment and several Antarctic lakes, especially Organic Lake and Ace Lake, where roseobacters are prevalent (Yau et al ., ; Zhan et al ., ).…”

“…N4‐like phages are highly diverse and prevalent in the winter Chesapeake Bay (Zhan et al ., ). A global survey on their distribution indicated that N4‐like phages appear to be restricted to the high latitude marine environment and several Antarctic lakes, especially Organic Lake and Ace Lake, where roseobacters are prevalent (Yau et al ., ; Zhan et al ., ). The presence of DSS3Φ8 in these Antarctic lakes further supports the tight co‐existence of roseobacters and their phages (Zhan et al ., ).…”

Isolation and characterization of bacteriophages with lytic activity against common bacterial pathogens

“…Bacteriophages are viruses which have the ability to multiply only in bacterial cells, and they are detectable almost everywhere where live bacteria exist [ 1 ]. The environment populated by bacterial hosts such as soil, sewage, and animal secretions are unique source of all types of phages, offering the possibility to isolate them for therapeutic purposes [ 2 ].…”