Diversity and Host Interactions among Virulent and Temperate Baltic Sea Flavobacterium Phages

Nilsson, Emelie; Bayfield, Oliver W.; Lundin, Daniel; Antson, A.A.; Holmfeldt, Karin

doi:10.3390/v12020158

Cited by 16 publications

(24 citation statements)

References 104 publications

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“…The genomes of the three phages isolated on the Flavobacterium strain LMO8 showed a minimum intergenomic similarity of 99.2% (Table S2) and were not related (<0.1% intergenomic similarity) to phages previously isolated from the same host strain (genera Tant ‐ and Pippivirus , Nilsson et al ., 2020). The most similar published phage genome was an uncultured single‐amplified genome, vSAG 37‐F16 retrieved from the Mediterranean Sea (Martinez‐Hernandez et al ., 2017), exhibiting a genome similarity of 5.1% to the three phages isolated on LMO8.…”

Section: Resultsmentioning

confidence: 99%

“…Phages previously isolated on Flavobacterium LMO8 were able to infect two other Flavobacterium strains, although these only shared 85% ANI with the original host (Nilsson et al ., 2020). In contrast, immuto_2‐6A isolated on LMO8 in this study did not infect any of the tested Flavobacteriaceae strains apart from its original host.…”

Section: Resultsmentioning

confidence: 99%

“…All originally counted plaques from the mesocosm samples displayed the same, tiny plaque morphology (dots, <1 mm), which differed from the plaque morphology of the previously known LMO8 phages (1–3 mm). Notably, phages for LMO8 have been isolated in low abundances compared to phages for other hosts during the same investigations (this study and Nilsson et al ., 2020), suggesting a low abundance in the Baltic Proper, where they may exist at the detection limit for conventional plaque assay methods. Detection of the immuto‐phages in viral metagenomes from LMO, where the maximum relative abundance was more than an order of magnitude lower than that of the elemo‐phages (see below, Fig.…”

Section: Resultsmentioning

confidence: 99%

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Dynamics of Baltic Sea phages driven by environmental changes

Hoetzinger

Nilsson

Arabi

et al. 2021

Environmental Microbiology

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Phage predation constitutes a major mortality factor for bacteria in aquatic ecosystems, and thus, directly impacts nutrient cycling and microbial community dynamics. Yet, the population dynamics of specific phages across time scales from days to months remain largely unexplored, which limits our understanding of their influence on microbial succession. To investigate temporal changes in diversity and abundance of phages infecting particular host strains, we isolated 121 phage strains that infected three bacterial hosts during a Baltic Sea mesocosm experiment. Genome analysis revealed a novel Flavobacterium phage genus harboring gene sets putatively coding for synthesis of modified nucleotides and glycosylation of bacterial cell surface components. Another novel phage genus revealed a microdiversity of phage species that was largely maintained during the experiment and across mesocosms amended with different nutrients. In contrast to the newly described Flavobacterium phages, phages isolated from a Rheinheimera strain were highly similar to previously isolated genotypes, pointing to genomic consistency in this population. In the mesocosm experiment, the investigated phages were mainly detected after a phytoplankton bloom peak. This concurred with recurrent detection of the phages in the Baltic Proper during summer months, suggesting an influence on the succession of heterotrophic bacteria associated with phytoplankton blooms.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Dynamics of Baltic Sea phages driven by environmental changes

Hoetzinger

Nilsson

Arabi

et al. 2021

Environmental Microbiology

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“…The Bacteroidetes are a ubiquitous phylum that is abundant throughout the oceans and known to associate with particles (Kirchman, 2008; Thomas et al ., 2011). Marine Bacteroidetes phages have been isolated for several genera (e.g., Cellulophaga , Croceibacter , Flavobacterium , and Polaribacter ; Borriss et al ., 2003; Holmfeldt et al ., 2007; Luhtanen et al ., 2014; Kang et al ., 2015; Kang et al ., 2016; Nilsson et al ., 2020). Cellulophaga baltica , a marine bacterium isolated from the Baltic Sea, and its lytic infecting phages has emerged as a model for understanding phage‐host dynamics among marine Bacterioidetes.…”

Section: Phage–host Interactions Of Cultured Model Marine Systemsmentioning

confidence: 99%

Lysogeny in the oceans: Lessons from cultivated model systems and a reanalysis of its prevalence

Tuttle

Buchan

2020

Environmental Microbiology

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In the oceans, viruses that infect bacteria (phages) influence a variety of microbially mediated processes that drive global biogeochemical cycles. The nature of their influence is dependent upon infection mode, be it lytic or lysogenic. Temperate phages are predicted to be prevalent in marine systems where they are expected to execute both types of infection modes. Understanding the range and outcomes of temperate phage-host interactions is fundamental for evaluating their ecological impact. Here, we (i) review phage-mediated rewiring of host metabolism, with a focus on marine systems, (ii) consider the range and nature of temperate phage-host interactions, and (iii) draw on studies of cultivated model systems to examine the consequences of lysogeny among several dominant marine bacterial lineages. We also readdress the prevalence of lysogeny among marine bacteria by probing a collection of 1239 publicly available bacterial genomes, representing cultured and uncultivated strains, for evidence of complete prophages. Our conservative analysis, anticipated to underestimate true prevalence, predicts 18% of the genomes examined contain at least one prophage, the majority (97%) were found within genomes of cultured isolates. These results highlight the need for cultivation of additional model systems to better capture the diversity of temperate phagehost interactions in the oceans.

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“…Abundances of viral genomes were estimated using coverage calculated across all samples using a method described by Roux et al ( 78 ). In short, reads were mapped using Bowtie2 ( 79 ) at ≥90% identity using the options –ignore-quals –mp = 1,1 –np = 1 –rdg = 0,1 –rfg = 0,1 –score-min = L,0,-0.1 as suggested by Nilsson et al ( 80 ). Coverages were calculated only for scaffolds with mapped reads across ≥75% of the scaffold length with ≥1× coverage, for which average per-base coverage was calculated.…”

Section: Methodsmentioning

confidence: 99%

Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil

et al. 2021

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Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show evidence of diverse viruses infecting a wide range of hosts found in sites up to 205 km apart. Viral genomes carried putative extremotolerance features (i.e., spore formation proteins) and auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. We propose a mutualistic model of host-virus interactions in the hyperarid core where viruses seek protection in microbial cells as lysogens or pseudolysogens, while viral extremotolerance genes aid survival of their hosts. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment. IMPORTANCE Deserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments, supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results demonstrate that diverse viruses are widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex virus-host interplay that shapes the unique microbiome in desert soils.

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Diversity and Host Interactions among Virulent and Temperate Baltic Sea Flavobacterium Phages

Cited by 16 publications

References 104 publications

Dynamics of Baltic Sea phages driven by environmental changes

Dynamics of Baltic Sea phages driven by environmental changes

Lysogeny in the oceans: Lessons from cultivated model systems and a reanalysis of its prevalence

Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil

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