Complete Genome Sequences of Five Bacteriophages That Infect Rhodobacter capsulatus

Bollivar, David; Bernardoni, Brooke; Bockman, Matthew R.; Miller, Brenda; Russell, Daniel A.; Delesalle, Véronique A.; Krukonis, Gregory P.; Hatfull, Graham F.; Cross, Madeline; Szewczyk, Marlena; Eppurath, Atul

doi:10.1128/genomea.00051-16

Cited by 12 publications

(10 citation statements)

References 9 publications

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“…Additionally, some patterns were sample or borough specific. For example, two Queens samples (9 and 15) both had viral contigs that clustered with Rhodobacter phage RcRhea known to infect the photosynthetic bacterium Rhodobacter capsulatus (22). Two samples from Brooklyn (4 and 5) clustered with Achromobacter phage JWF, which was recently isolated from sewage and found to infect the bacterium Achromobacter xylosoxidans, an emerging nosocomial pathogen typically found in wet environments (23).…”

Section: Resultsmentioning

confidence: 99%

Initial Mapping of the New York City Wastewater Virome

et al. 2020

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Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments. IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.

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Section: Resultsmentioning

confidence: 99%

Initial Mapping of the New York City Wastewater Virome

et al. 2020

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“…Searches conducted using dc-megablast and megablast revealed significant nucleotide similarity between Loki and Acinetobacter phage IME_AB3 and these two phages exhibit significant synteny across the entire genome. Additional relationships with Burkholderia phage vB_BceS_KL1 [ 12 ], Paracoccus phage vB_PmaS_IMEP1, Stenotrophomonas phages DLP1 and DLP2 [ 43 ], Rhodobacter phages RcTitan and RcSpartan [ 45 ], as well as Pseudomonas phages vB_Pae_Kakheti25 [ 46 ], vB_PaeS_SCH_Ab26 and PA73 [ 47 ] were also identified using TBLASTX. To perform pairwise comparisons, genomes were co-linearised to start at the small terminase subunit and aligned using ClustalX ( Fig 5A ) and EMBOSS Stretcher ( Fig 5B ).…”

Section: Resultsmentioning

confidence: 99%

Characterisation and genome sequence of the lytic Acinetobacter baumannii bacteriophage vB_AbaS_Loki

et al. 2017

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Acinetobacter baumannii has emerged as an important nosocomial pathogen in healthcare and community settings. While over 100 of Acinetobacter phages have been described in the literature, relatively few have been sequenced. This work describes the characterisation and genome annotation of a new lytic Acinetobacter siphovirus, vB_AbaS_Loki, isolated from activated sewage sludge. Sequencing revealed that Loki encapsulates a 41,308 bp genome, encoding 51 predicted open reading frames. Loki is most closely related to Acinetobacter phage IME_AB3 and more distantly related to Burkholderia phage KL1, Paracoccus phage vB_PmaS_IMEP1 and Pseudomonas phages vB_Pae_Kakheti25, vB_PaeS_SCH_Ab26 and PA73. Loki is characterised by a narrow host range, among the 40 Acinetobacter isolates tested, productive infection was only observed for the propagating host, A. baumannii ATCC 17978. Plaque formation was found to be dependent upon the presence of Ca2+ ions and adsorption to host cells was abolished upon incubation with a mutant of ATCC 17978 encoding a premature stop codon in lpxA. The complete genome sequence of vB_AbaS_Loki was deposited in the European Nucleotide Archive (ENA) under the accession number LN890663.

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“…Four phages have very low numbers of shared genes and are described as singletons following the terminology of Hatfull et al (27). It also should be noted that two clusters have also been described as Genera; RcA is the genus Cronusvirus , and RcB is the genus Titanvirus (28–30).…”

Section: Resultsmentioning

confidence: 99%

“…RcRhea and RcCronus have the exact same set of 45 genes while RcSaxon has two novel genes (orphams) where the other two have just one (gene 25 in both RcRhea and RcCronus; genes 25 and 26 in RcSaxon). Genome sequences of these phages were reported in a genome announcement (30) and led to the creation of a phage genus, Cronusvirus, with RcCronus considered the type phage for the genus (28).…”

Section: Resultsmentioning

confidence: 99%

Genomic diversity of bacteriophages infecting Rhodobacter capsulatus and their relatedness to its gene transfer agent RcGTA

Rapala

Miller

Garcia

et al. 2021

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The diversity of bacteriophages is likely unparalleled in the biome due to the immense variety of hosts and the multitude of viruses that infect them. Recent efforts have led to description at the genomic level of numerous bacteriophages that infect the Actinobacteria, but relatively little is known about those infecting other prokaryotic phyla, such as the purple non-sulfur photosynthetic α-proteobacterium Rhodobacter capsulatus. This species is a common inhabitant of freshwater ecosystems and has been an important model system for the study of photosynthesis. Additionally, it is notable for its utilization of a unique form of horizontal gene transfer via a bacteriophage-like element known as the gene transfer agent (RcGTA). Only three bacteriophages of R. capsulatus had been sequenced prior to this report. Isolation and characterization at the genomic level of 26 new bacteriophages infecting this host advances the understanding of bacteriophage diversity and the origins of RcGTA. These newly discovered isolates can be grouped along with three that were previously sequenced to form six clusters with four remaining as single representatives. These bacteriophages share genes with RcGTA that seem to be related to host recognition. One isolate was found to cause lysis of a marine bacterium when exposed to high titer lysate. Although some clusters are more highly represented in the sequenced genomes, it is evident that many more bacteriophage types that infect R. capsulatus are likely to be found in the future.

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Complete Genome Sequences of Five Bacteriophages That Infect Rhodobacter capsulatus

Cited by 12 publications

References 9 publications

Initial Mapping of the New York City Wastewater Virome

Initial Mapping of the New York City Wastewater Virome

Characterisation and genome sequence of the lytic Acinetobacter baumannii bacteriophage vB_AbaS_Loki

Genomic diversity of bacteriophages infecting Rhodobacter capsulatus and their relatedness to its gene transfer agent RcGTA

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