Exploring Phage Ecology, Genetics, and Impact in Food Fermentations

2014 ◽  
pp. 92-113
Keyword(s):  
Phage Ecology

scholarly journals Lifestyle of sponge symbiont phages by host prediction and correlative microscopy

2021 ◽  
Author(s):  
M. T. Jahn ◽  
T. Lachnit ◽  
S. M. Markert ◽  
C. Stigloher ◽  
L. Pita ◽  
...  
Keyword(s):  
Distinct Pattern ◽  
Microbial Consortia ◽  
Bacterial Symbionts ◽  
Correlative Microscopy ◽  
Phage Ecology ◽  
Infection Dynamics ◽  
Imaging Approach ◽  
Animal Hosts ◽  
Viral Distribution

AbstractBacteriophages (phages) are ubiquitous elements in nature, but their ecology and role in animals remains little understood. Sponges represent the oldest known extant animal-microbe symbiosis and are associated with dense and diverse microbial consortia. Here we investigate the tripartite interaction between phages, bacterial symbionts, and the sponge host. We combined imaging and bioinformatics to tackle important questions on who the phage hosts are and what the replication mode and spatial distribution within the animal is. This approach led to the discovery of distinct phage-microbe infection networks in sponge versus seawater microbiomes. A new correlative in situ imaging approach (‘PhageFISH-CLEM‘) localised phages within bacterial symbiont cells, but also within phagocytotically active sponge cells. We postulate that the phagocytosis of free virions by sponge cells modulates phage-bacteria ratios and ultimately controls infection dynamics. Prediction of phage replication strategies indicated a distinct pattern, where lysogeny dominates the sponge microbiome, likely fostered by sponge host-mediated virion clearance, while lysis dominates in seawater. Collectively, this work provides new insights into phage ecology within sponges, highlighting the importance of tripartite animal-phage-bacterium interplay in holobiont functioning. We anticipate that our imaging approach will be instrumental to further understanding of viral distribution and cellular association in animal hosts.

Aquatic phage ecology

2009 ◽  
pp. 251-280 ◽  
Author(s):  
T. Frede Thingstad ◽  
Gunnar Bratbak ◽  
Mikal Heldal
Keyword(s):  
Phage Ecology

Phage Ecological Hiatus Ends Phage Ecology S. M. Goyal C. P. Gerga G. Britton

BioScience ◽  
1989 ◽  
Vol 39 (3) ◽  
pp. 189-190
Author(s):  
Richard E. Ford
Keyword(s):  
Phage Ecology

scholarly journals Bacteriophage adaptation to a mammalian mucosa reveals a trans–domain evolutionary axis

2021 ◽  
Author(s):  
Wai Hoe Chin ◽  
Ciaren Kett ◽  
Oren Cooper ◽  
Deike Müseler ◽  
Yaqi Zhang ◽  
...  
Keyword(s):  
De Novo ◽  
Genetic Recombination ◽  
Evolutionary Relationship ◽  
Mammalian Host ◽  
Single Mutation ◽  
Phage Ecology ◽  
Fitness Advantage ◽  
Gut Mucosa

The majority of viruses within the human gut are obligate bacterial viruses known as bacteriophages (phages)1. Their bacteriotropism underscores the study of phage ecology in the gut, where they sustain top–down control2—4 and co–evolve5 with gut bacterial communities. Traditionally, these were investigated empirically via in vitro experimental evolution6—8 and more recently, in vivo models were adopted to account for gut niche effects4,9. Here, we probed beyond conventional phage–bacteria co–evolution to investigate the potential evolutionary interactions between phages and the mammalian ″host″. To capture the role of the mammalian host, we recapitulated a life–like mammalian gut mucosa using in vitro lab–on–a–chip devices (to wit, the gut–on–a–chip) and showed that the mucosal environment supports stable phage–bacteria co–existence. Next, we experimentally evolved phage populations within the gut–on–a–chip devices and discovered that phages adapt by de novo mutations and genetic recombination. We found that a single mutation in the phage capsid protein Hoc — known to facilitate phage adherence to mucus10 — caused altered phage binding to fucosylated mucin glycans. We demonstrated that the altered glycan–binding phenotype provided the evolved mutant phage a competitive fitness advantage over their ancestral wildtype phage in the gut–on–a–chip mucosal environment. Collectively, our findings revealed that phages — in addition to their evolutionary relationship with bacteria — are also able to engage in evolution with the mammalian host.

scholarly journals Seasonal Population Dynamics and Interactions of Competing Bacteriophages and Their Host in the Rhizosphere

2000 ◽  
Vol 66 (10) ◽  
pp. 4193-4199 ◽  
Author(s):  
Kevin E. Ashelford ◽  
Susan J. Norris ◽  
John C. Fry ◽  
Mark J. Bailey ◽  
Martin J. Day
Keyword(s):  
Sugar Beet ◽  
Latin Square ◽  
Optimal Foraging Theory ◽  
Microbial Interactions ◽  
Phage Ecology ◽  
Competitive Disadvantage ◽  
First Time ◽  
Field Plots ◽  
Seasonal Population

ABSTRACT We describe two prolonged bacteriophage blooms within sugar beet rhizospheres ensuing from an artificial increase in numbers of an indigenous soil bacterium. Further, we provide evidence of in situ competition between these phages. This is the first in situ demonstration of such microbial interactions in soil. To achieve this, sugar beet seeds were inoculated with Serratia liquefaciensCP6RS or its lysogen, CP6RS-ly-Φ1. These were sown, along with uninoculated seeds, in 36 field plots arranged in a randomized Latin square. The plots were then sampled regularly over 194 days, and the plants were assayed for the released bacteria and any infectious phages. Both the lysogen and nonlysogen forms of CP6RS survived equally well in situ, contradicting earlier work suggesting lysogens have a competitive disadvantage in nature. A Podoviridae phage, identified as ΦCP6-4, flourished on the nonlysogen-inoculated plants in contrast to those plants inoculated with the lysogen. Conversely, the Siphoviridae phage ΦCP6-1 (used to construct the released lysogen) was isolated abundantly from the lysogen-treated plants but almost never on the nonlysogen-inoculated plants. The uninoculated plants also harbored some ΦCP6-1 phage up to day 137, yet hardly any ΦCP6-4 phages were found, and this was consistent with previous years. We show that the different temporal and spatial distributions of these two physiologically distinct phages can be explained by application of optimal foraging theory to phage ecology. This is the first time that such in situ evidence has been provided in support of this theoretical model.

scholarly journals Community context matters for bacteria-phage ecology and evolution

2021 ◽  
Author(s):  
Michael Blazanin ◽  
Paul E. Turner
Keyword(s):  
Bacterial Community ◽  
Bacterial Species ◽  
Community Context ◽  
Ecological Interactions ◽  
Biological Models ◽  
Phage Ecology ◽  
Additional Investigation ◽  
Mechanisms Of Adaptation ◽  
Community Presence

Bacteria-phage symbioses are ubiquitous in nature and serve as valuable biological models. Historically, the ecology and evolution of bacteria-phage systems have been studied in either very simple or very complex communities. Although both approaches provide insight, their shortcomings limit our understanding of bacteria and phages in multispecies contexts. To address this gap, here we synthesize the emerging body of bacteria-phage experiments in medium-complexity communities, specifically those that manipulate bacterial community presence. Generally, community presence suppresses both focal bacterial (phage host) and phage densities, while sometimes altering bacteria-phage ecological interactions in diverse ways. Simultaneously, community presence can have an array of evolutionary effects. Sometimes community presence has no effect on the coevolutionary dynamics of bacteria and their associated phages, whereas other times the presence of additional bacterial species constrains bacteria-phage coevolution. At the same time, community context can alter mechanisms of adaptation and interact with the pleiotropic consequences of (co)evolution. Ultimately, these experiments show that community context can have important ecological and evolutionary effects on bacteria-phage systems, but many questions still remain unanswered and ripe for additional investigation.

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