Dynamics of infection in a novel group of promiscuous phages and hosts of multiple bacterial genera retrieved from river communities

AbstractPhages are generally described as species- or even strain-specific viruses, implying an inherent limitation for some to be maintained and spread in diverse bacterial communities. Moreover, phage isolation and host range determination rarely consider the phage ecological context, likely biasing our notion on phage specificity. Here we identified and characterized a novel group of promiscuous phages existing in rivers by using diverse bacteria isolated from the same samples, and then used this biological system to investigate infection dynamics in distantly related hosts. We assembled a diverse collection of over 600 native bacterial strains and used them to isolate six podophages, named Atoyac, from different geographic origin and capable of infecting six genera in the Gammaproteobacteria. Atoyac phage genomes are highly similar to each other but not to those currently available in the genome and metagenome public databases. Detailed comparison of the phage’s infectivity in diverse hosts and trough hundreds of interactions revealed variation in plating efficiency amongst bacterial genera, implying a cost associated with infection of distant hosts, and between phages, despite their sequence similarity. We show, through experimental evolution in single or alternate hosts of different genera, that plaque production efficiency is highly dynamic and tends towards optimization in hosts rendering low plaque formation. Complex adaptation outcomes observed in the evolution experiments differed between highly similar phages and suggest that propagation in multiple hosts may be key to maintain promiscuity in some viruses. Our study expands our knowledge of the virosphere and uncovers bacteria-phage interactions overlooked in natural systems.ImportanceIn natural environments, phages co-exist and interact with a broad variety of bacteria, posing a conundrum for narrow-host-range phages maintenance in diverse communities. This context is rarely considered in the study of host-phage interactions, typically focused on narrow-host-range viruses and their infectivity in target bacteria isolated from sources distinct to where the phages were retrieved from. By studying phage-host interactions in bacteria and viruses isolated from river microbial communities, we show that novel phages with promiscuous host range encompassing multiple bacterial genera can be found in the environment. Assessment of hundreds of interactions in diverse hosts revealed that similar phages exhibit different infection efficiency and adaptation patterns. Understanding host range is fundamental in our knowledge of bacteria-phage interactions and their impact in microbial communities. The dynamic nature of phage promiscuity revealed in our study has implications in different aspects of phage research such as horizontal gene transfer or phage therapy.

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Resolving the structure of phage-bacteria interactions in the context of natural diversity

10.1101/2021.06.27.449121 ◽

2021 ◽

Author(s):

Kathryn M Kauffman ◽

William K Chang ◽

Julia M Brown ◽

Fatima Aysha Hussain ◽

Joy Y Yang ◽

...

Keyword(s):

Microbial Communities ◽

Host Range ◽

Large Scale ◽

Genomic Diversity ◽

Interaction Networks ◽

Bacterial Strains ◽

Quantitative Estimates ◽

Phage Evolution ◽

Marine Vibrio ◽

In The Wild

Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in "the wild" remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain quantitative estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that killing in environmental interaction networks is sparse - with phage predator loads low for most bacterial strains and phages host-strain-specific in their killing. Paradoxically, we also find that although overlap in killing is generally rare between phages, recombination is common. Together, these results indicate that the number of hosts that phages infect is often larger than the number that they kill and suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it will be important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on killing host range.

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Isolation of Potential Phages against Multidrug-Resistant Bacterial Isolates: Promising Agents in the Rivers of Kathmandu, Nepal

BioMed Research International ◽

10.1155/2017/3723254 ◽

2017 ◽

Vol 2017 ◽

pp. 1-10 ◽

Cited By ~ 2

Author(s):

Anjeela Bhetwal ◽

Anjila Maharjan ◽

Shreena Shakya ◽

Deepa Satyal ◽

Sumitra Ghimire ◽

...

Keyword(s):

Host Range ◽

River Water ◽

Water Samples ◽

Multidrug Resistant ◽

Potential Effect ◽

Broad Host Range ◽

Bacterial Strains ◽

Clinical Strains ◽

Narrow Host Range ◽

The Subject

Bacteriophages are being the subject of interest for alternative antimicrobial therapy for infectious diseases in recent years. Therapeutic effectiveness regarding phage therapy is a matter of concern since it is the most promising biological treatment of this era. Hence, the present study was aimed to isolate the potential bacteriophages present in river water samples and to analyze their host range among clinical strains of bacteria. Ten different locations of Kathmandu valley were selected for the collection of river water for the detection of probable phages. Bacteriophages were isolated from water samples using the double agar overlay method. Isolated phages were purified by diluting in the SM-buffer and filtering through 0.22 μm filter. Purified lysate was further processed for analyzing its host range by using spot method. Their host range was characterized against 20 bacterial strains, including multidrug-resistant. Total 67 different phages were isolated against 8 different host organisms. Out of them, forty-seven phages were selected for analyzing its host range. Among them, Serratia phages (ΦSER) had the broad host range infecting 17 different bacterial strains including multidrug-resistant harboring ESBL and MBL genotypes. However, Klebsiella phages (ΦKP) had narrow host range in comparison to other phages. Isolated phages had the potential effect against clinical strains of bacteria along with their broader host spectrum. Most importantly, promising effect against MDR pathogens in this study has raised the probable chances of the utility of these phages for biological control of bacterial infection including MBL and ESBL strains.

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A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation

mSystems ◽

10.1128/msystems.00773-20 ◽

2021 ◽

Vol 6 (1) ◽

Cited By ~ 2

Author(s):

Daniel Cazares ◽

Adrian Cazares ◽

Wendy Figueroa ◽

Gabriel Guarneros ◽

Robert A. Edwards ◽

...

Keyword(s):

Host Range ◽

Host Adaptation ◽

Natural Environments ◽

Narrow Host Range ◽

Diverse Communities ◽

Broad Variety ◽

River Communities

In natural environments, phages coexist and interact with a broad variety of bacteria, posing a conundrum for narrow-host-range phage maintenance in diverse communities. This context is rarely considered in the study of host-phage interactions, typically focused on narrow-host-range viruses and their infectivity in target bacteria isolated from sources distinct to where the phages were retrieved from.

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Effect of Iron Limitation on the Ultrastructure of Agmenellum Quadruplicatum

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100098551 ◽

1981 ◽

Vol 39 ◽

pp. 410-411

Author(s):

L. P. Hardie ◽

D. L. Balkwill ◽

S. E. Stevens

Keyword(s):

Growth Medium ◽

Green Alga ◽

Natural Habitat ◽

Iron Limitation ◽

Natural Environments ◽

Blue Green Alga ◽

Marine Cyanobacterium ◽

Natural Systems ◽

Thin Sectioning ◽

Agmenellum Quadruplicatum

Agmenellum quadruplicatum is a unicellular, non-nitrogen-fixing, marine cyanobacterium (blue-green alga). The ultrastructure of this organism, when grown in the laboratory with all necessary nutrients, has been characterized thoroughly. In contrast, little is known of its ultrastructure in the specific nutrient-limiting conditions typical of its natural habitat. Iron is one of the nutrients likely to limit this organism in such natural environments. It is also of great importance metabolically, being required for both photosynthesis and assimilation of nitrate. The purpose of this study was to assess the effects (if any) of iron limitation on the ultrastructure of A. quadruplicatum. It was part of a broader endeavor to elucidate the ultrastructure of cyanobacteria in natural systemsActively growing cells were placed in a growth medium containing 1% of its usual iron. The cultures were then sampled periodically for 10 days and prepared for thin sectioning TEM to assess the effects of iron limitation.

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Deconstruction of Lignin: From Enzymes to Microorganisms

Molecules ◽

10.3390/molecules26082299 ◽

2021 ◽

Vol 26 (8) ◽

pp. 2299

Author(s):

Jéssica P. Silva ◽

Alonso R. P. Ticona ◽

Pedro R. V. Hamann ◽

Betania F. Quirino ◽

Eliane F. Noronha

Keyword(s):

Microbial Communities ◽

Metabolic Pathways ◽

Low Cost ◽

Direct Analysis ◽

Industrial Applications ◽

Natural Environments ◽

Lignocellulosic Residues ◽

Complementary Techniques ◽

Plant Polymer ◽

Powerful Strategy

Lignocellulosic residues are low-cost abundant feedstocks that can be used for industrial applications. However, their recalcitrance currently makes lignocellulose use limited. In natural environments, microbial communities can completely deconstruct lignocellulose by synergistic action of a set of enzymes and proteins. Microbial degradation of lignin by fungi, important lignin degraders in nature, has been intensively studied. More recently, bacteria have also been described as able to break down lignin, and to have a central role in recycling this plant polymer. Nevertheless, bacterial deconstruction of lignin has not been fully elucidated yet. Direct analysis of environmental samples using metagenomics, metatranscriptomics, and metaproteomics approaches is a powerful strategy to describe/discover enzymes, metabolic pathways, and microorganisms involved in lignin breakdown. Indeed, the use of these complementary techniques leads to a better understanding of the composition, function, and dynamics of microbial communities involved in lignin deconstruction. We focus on omics approaches and their contribution to the discovery of new enzymes and reactions that impact the development of lignin-based bioprocesses.

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Influence of biopolymers on the rheological properties of seafloor sediments and the runout behavior of submarine debris flows

Scientific Reports ◽

10.1038/s41598-021-81186-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jun Kameda ◽

Hamada Yohei

Keyword(s):

Rheological Properties ◽

Debris Flows ◽

Extracellular Polymeric Substances ◽

Flow Behavior ◽

Mass Movement ◽

Rheological Parameters ◽

Natural Environments ◽

Natural Systems ◽

Chemical Conditions ◽

Seafloor Sediments

AbstractSubmarine debris flows are mass movement processes on the seafloor, and are geohazards for seafloor infrastructure such as pipelines, communication cables, and submarine structures. Understanding the generation and run-out behavior of submarine debris flows is thus critical for assessing the risk of such geohazards. The rheological properties of seafloor sediments are governed by factors including sediment composition, grain size, water content, and physico-chemical conditions. In addition, extracellular polymeric substances (EPS) generated by microorganisms can affect rheological properties in natural systems. Here we show that a small quantity of EPS (~ 0.1 wt%) can potentially increase slope stability and decrease the mobility of submarine debris flows by increasing the internal cohesion of seafloor sediment. Our experiments demonstrated that the flow behavior of sediment suspensions mixed with an analogue material of EPS (xanthan gum) can be described by a Herschel–Bulkley model, with the rheological parameters being modified progressively, but not monotonously, with increasing EPS content. Numerical modeling of debris flows demonstrated that the run-out distance markedly decreases if even 0.1 wt% of EPS is added. The addition of EPS can also enhance the resistivity of sediment to fluidization triggered by cyclic loading, by means of formation of an EPS network that binds sediment particles. These findings suggest that the presence of EPS in natural environments reduces the likelihood of submarine geohazards.

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Phenotypically and Genotypically Heterogeneous Strains of Pseudomonas syringae Associated With Alfalfa Leaf Spot Disease in Iran

Plant Disease ◽

10.1094/pdis-06-19-1153-re ◽

2019 ◽

Vol 103 (12) ◽

pp. 3199-3208 ◽

Cited By ~ 2

Author(s):

Maryam Ansari ◽

S. Mohsen Taghavi ◽

Sadegh Zarei ◽

Soraya Mehrb-Moghadam ◽

Hamzeh Mafakheri ◽

...

Keyword(s):

Host Range ◽

Pseudomonas Syringae ◽

Leaf Spot ◽

Phylogenetic Analyses ◽

Housekeeping Genes ◽

Pcr Primers ◽

Phylogenetic Position ◽

Leaf Spot Disease ◽

Bacterial Strains ◽

Alfalfa Leaf

In this study, we provide a polyphasic characterization of 18 Pseudomonas spp. strains associated with alfalfa leaf spot symptoms in Iran. All of the strains were pathogenic on alfalfa, although the aggressiveness and symptomology varied among the strains. All strains but one were pathogenic on broad bean, cucumber, honeydew, and zucchini, whereas only a fraction of the strains were pathogenic on sugar beet, tomato, and wheat. Syringomycin biosynthesis genes (syrB1 and syrP) were detected using the corresponding PCR primers in all of the strains isolated from alfalfa. Phylogenetic analyses using the sequences of four housekeeping genes (gapA, gltA, gyrB, and rpoD) revealed that all of the strains except one (Als34) belong to phylogroup 2b of P. syringae sensu lato, whereas strain Als34 placed within phylogroup 1 close to the type strain of P. syringae pv. apii. Among the phylogroup 2b strains, nine strains were phylogenetically close to the P. syringae pv. aptata clade, whereas the remainder were scattered among P. syringae pv. atrofaciens and P. syringae pv. syringae strains. Pathogenicity and host range assays of the bacterial strains evaluated in this study on a set of taxonomically diverse plant species did not allow us to assign a “pathovar” status to the alfalfa strains. However, these results provide novel insight into the host range and phylogenetic position of the alfalfa-pathogenic members of P. syringae sensu lato, and they reveal that phenotypically and genotypically heterogeneous strains of the pathogen cause bacterial leaf spot of alfalfa.

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Umboniibacter marinipuniceus gen. nov., sp. nov., a marine gammaproteobacterium isolated from the mollusc Umbonium costatum from the Sea of Japan

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.010728-0 ◽

2010 ◽

Vol 60 (3) ◽

pp. 603-609 ◽

Cited By ~ 12

Author(s):

Lyudmila A. Romanenko ◽

Naoto Tanaka ◽

Galina M. Frolova

Keyword(s):

Sea Of Japan ◽

Sequence Similarity ◽

Fatty Acid Analysis ◽

Phenotypic Characterization ◽

The Sea Of Japan ◽

Rrna Gene ◽

Phylogenetic Distance ◽

The Novel ◽

Bacterial Strains ◽

Separate Branch

Two bacterial strains, KMM 3891T and KMM 3892, were isolated from internal tissues of the marine mollusc Umbonium costatum collected from the Sea of Japan. The novel isolates were Gram-negative, aerobic, faint pink–reddish-pigmented, rod-shaped, non-motile, stenohaline and psychrotolerant bacteria that were unable to degrade most tested complex polysaccharides. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Fatty acid analysis revealed C17 : 1 ω6c, C17 : 0, C16 : 0 and C16 : 1 ω7c as the dominant components. The major isoprenoid quinone was Q-7. The DNA G+C content of strain KMM 3891T was 51.7 mol%. According to phylogenetic analysis of 16S rRNA gene sequences, strains KMM 3891T and KMM 3892 were positioned within the Gammaproteobacteria as a separate branch, sharing <93 % sequence similarity to their phylogenetic relatives including Saccharophagus degradans, Microbulbifer species, Endozoicomonas elysicola, Simiduia agarivorans and Teredinibacter turnerae. Based on phenotypic characterization and phylogenetic distance, the novel marine isolates KMM 3891T and KMM 3892 represent a new genus and species, for which the name Umboniibacter marinipuniceus gen. nov., sp. nov. is proposed. The type strain of Umboniibacter marinipuniceus is KMM 3891T (=NRIC 0753T =JCM 15738T).

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Screening and Isolation of Bacterial Strains with the Biotechnological Potential to Destruct Cyanide-Bearing Compounds under the Conditions of Extreme Continental Climate

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.1130.19 ◽

2015 ◽

Vol 1130 ◽

pp. 19-22

Author(s):

M.P. Belykh ◽

S.V. Petrov ◽

V.F. Petrov ◽

A.Yu. Chikin ◽

N.L. Belkova

Keyword(s):

Microbial Communities ◽

Gold Mining ◽

Molecular Genetic ◽

Heap Leaching ◽

Bacterial Strains ◽

Mining Operations ◽

Biotechnological Potential ◽

Enriched Cultures ◽

Continental Climate

The methods of biodegradation are of special interest because they help solving environmental problems of wastes detoxification from gold-mining operations. The use of bacterial strains is a promising approach in the field of biotechnology to destruct cyanide-bearing compounds. The diversity of microbial communities both in heap in situ and in the enriched cultures was studied with molecular genetic methods. The differences in representation of bacteria, cultivated in unexploitable and operating heaps, are territory, site and heap specific. The strains of Pseudomonas sp. and Methylobacterium sp. possess the biotechnological potential and might be used in biodegradation of heap leaching wastes in extreme continental climate.

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