The Sisal Virome: Uncovering the Viral Diversity of Agave Varieties Reveals New and Organ-Specific Viruses

Gabriel Quintanilha-Peixoto; Paula Luize Camargos Fonseca; Fábio Trigo Raya; Marina Pupke Marone; Dener Eduardo Bortolini; Piotr Mieczkowski; Roenick Proveti Olmo; Marcelo Falsarella Carazzolle; Christian A. Voigt; Ana Cristina Fermino Soares; Gonçalo Amarante Guimarães Pereira; Aristóteles Góes-Neto; Eric Roberto Guimarães Rocha Aguiar

doi:10.3390/microorganisms9081704

The Sisal Virome: Uncovering the Viral Diversity of Agave Varieties Reveals New and Organ-Specific Viruses

Microorganisms ◽

10.3390/microorganisms9081704 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1704

Author(s):

Gabriel Quintanilha-Peixoto ◽

Paula Luize Camargos Fonseca ◽

Fábio Trigo Raya ◽

Marina Pupke Marone ◽

Dener Eduardo Bortolini ◽

...

Keyword(s):

Economic Value ◽

Systemic Infection ◽

Lower Number ◽

Taxa Richness ◽

Fiber Extraction ◽

Organ Specific ◽

Plant Microbiota ◽

Natural Leaf ◽

Agave Sisalana ◽

Rna And Dna

Sisal is a common name for different plant varieties in the genus Agave (especially Agave sisalana) used for high-quality natural leaf fiber extraction. Despite the economic value of these plants, we still lack information about the diversity of viruses (virome) in non-tequilana species from the genus Agave. In this work, by associating RNA and DNA deep sequencing we were able to identify 25 putative viral species infecting A. sisalana, A. fourcroydes, and Agave hybrid 11648, including one strain of Cowpea Mild Mottle Virus (CPMMV) and 24 elements likely representing new viruses. Phylogenetic analysis indicated they belong to at least six viral families: Alphaflexiviridae, Betaflexiviridae, Botourmiaviridae, Closteroviridae, Partitiviridae, Virgaviridae, and three distinct unclassified groups. We observed higher viral taxa richness in roots when compared to leaves and stems. Furthermore, leaves and stems are very similar diversity-wise, with a lower number of taxa and dominance of a single viral species. Finally, approximately 50% of the identified viruses were found in all Agave organs investigated, which suggests that they likely produce a systemic infection. This is the first metatranscriptomics study focused on viral identification in species from the genus Agave. Despite having analyzed symptomless individuals, we identified several viruses supposedly infecting Agave species, including organ-specific and systemic species. Surprisingly, some of these putative viruses are probably infecting microorganisms composing the plant microbiota. Altogether, our results reinforce the importance of unbiased strategies for the identification and monitoring of viruses in plant species, including those with asymptomatic phenotypes.

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Pathogen clonal expansion underlies multiorgan dissemination and organ-specific outcomes during systemic infection

10.1101/2021.05.17.444473 ◽

2021 ◽

Author(s):

Karthik Hullahalli ◽

Matthew K Waldor

Keyword(s):

Genetic Factors ◽

Systemic Infection ◽

Clonal Expansion ◽

Inoculum Size ◽

Pathogen Population ◽

E Coli ◽

Highly Sensitive ◽

Organ Specific ◽

Bacterial Genetic ◽

Pathogen Populations

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Pathogen clonal expansion underlies multiorgan dissemination and organ-specific outcomes during murine systemic infection

eLife ◽

10.7554/elife.70910 ◽

2021 ◽

Vol 10 ◽

Author(s):

Karthik Hullahalli ◽

Matthew K Waldor

Keyword(s):

Population Biology ◽

Cell Envelope ◽

Systemic Infection ◽

Clonal Expansion ◽

Inoculum Size ◽

Pathogen Population ◽

Infection Dynamics ◽

Specific Pathogen ◽

Organ Specific ◽

Bacterial Replication

The dissemination of pathogens through blood and their establishment within organs lead to severe clinical outcomes. However, the within-host dynamics that underly pathogen spread to and clearance from systemic organs remain largely uncharacterized. In animal models of infection, the observed pathogen population results from the combined contributions of bacterial replication, persistence, death, and dissemination, each of which can vary across organs. Quantifying the contribution of each these processes is required to interpret and understand experimental phenotypes. Here, we leveraged STAMPR, a new barcoding framework, to investigate the population dynamics of extraintestinal pathogenic E. coli, a common cause of bacteremia, during murine systemic infection. We show that while bacteria are largely cleared by most organs, organ-specific clearance failures are pervasive and result from dramatic expansions of clones representing less than 0.0001% of the inoculum. Clonal expansion underlies the variability in bacterial burden between animals, and stochastic dissemination of clones profoundly alters the pathogen population structure within organs. Despite variable pathogen expansion events, host bottlenecks are consistent yet highly sensitive to infection variables, including inoculum size and macrophage depletion. We adapted our barcoding methodology to facilitate multiplexed validation of bacterial fitness determinants identified with transposon mutagenesis and confirmed the importance of bacterial hexose metabolism and cell envelope homeostasis pathways for organ-specific pathogen survival. Collectively our findings provide a comprehensive map of the population biology that underlies bacterial systemic infection and a framework for barcode-based high-resolution mapping of infection dynamics.

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Chlorophyll, Chloroplast Ribosomal RNA, and DNA Are Reduced by Barley Stripe Mosaic Virus Systemic Infection

Phytopathology ◽

10.1094/phyto-78-570 ◽

1988 ◽

Vol 78 (5) ◽

pp. 570 ◽

Cited By ~ 13

Author(s):

Myron K. Brakke

Keyword(s):

Mosaic Virus ◽

Ribosomal Rna ◽

Systemic Infection ◽

Barley Stripe Mosaic Virus ◽

Rna And Dna

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Salmonella-induced thrombi in mice develop asynchronously in the spleen and liver and are not effective bacterial traps

Blood ◽

10.1182/blood-2018-08-867267 ◽

2019 ◽

Vol 133 (6) ◽

pp. 600-604 ◽

Cited By ~ 12

Author(s):

Nonantzin Beristain-Covarrubias ◽

Marisol Perez-Toledo ◽

Adriana Flores-Langarica ◽

Malou Zuidscherwoude ◽

Jessica R. Hitchcock ◽

...

Keyword(s):

Systemic Infection ◽

Organ Damage ◽

Multiple Organ ◽

Bacterial Burden ◽

Monocytic Cell ◽

Organ Specific ◽

Life Threatening ◽

Platelet Aggregates

Abstract Thrombosis is a frequent, life-threatening complication of systemic infection associated with multiple organ damage. We have previously described a novel mechanism of inflammation-driven thrombosis induced by Salmonella Typhimurium infection of mice. Thrombosis in the liver develops 7 days after infection, persisting after the infection resolves, and is monocytic cell dependent. Unexpectedly, thrombosis was not prominent in the spleen at this time, despite carrying a similar bacterial burden as the liver. In this study, we show that thrombosis does occur in the spleen but with strikingly accelerated kinetics compared with the liver, being evident by 24 hours and resolving rapidly thereafter. The distinct kinetics of thrombosis and bacterial burden provides a test of the hypothesis that thrombi form in healthy vessels to trap or remove bacteria from the circulation, often termed immunothrombosis. Remarkably, despite bacteria being detected throughout infected spleens and livers in the early days of infection, immunohistological analysis of tissue sections show that thrombi contain very low numbers of bacteria. In contrast, bacteria are present throughout platelet aggregates induced by Salmonella in vitro. Therefore, we show that thrombosis develops with organ-specific kinetics and challenge the universality of immunothrombosis as a mechanism to capture bacteria in vivo.

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CULTIVATION OF Caesalpiniapulcherrima L. Sw. IN REGIONAL SUBSTRATES

Revista Árvore ◽

10.1590/1806-90882018000200012 ◽

2018 ◽

Vol 42 (2) ◽

Cited By ~ 3

Author(s):

Flávia Mélo Moreira ◽

Rafaela Simão Abrahão Nóbrega ◽

Ronaldo Pedreira dos Santos ◽

Caeline Castor da Silva ◽

Júlio César Azevedo Nóbrega

Keyword(s):

Dry Weight ◽

Animal Manure ◽

Urban Waste ◽

Fiber Extraction ◽

Different Types ◽

Number Of Leaves ◽

Tree Pruning ◽

Agave Sisalana ◽

Dickson Quality Index

ABSTRACT The objective of the present research was to evaluate different types and proportions of organic wates and soil classes for substrate formulation for Caesalpinia pulcherrima cultivation. The experiment was performed in a greenhouse, and treatments were composed by two soil classes (Oxisol and Entisols), three types of residues (organic compound from pruning + manure, urban waste compost and residue from the extraction of Agave sisalana fibers) and five residue:soil proportions (0:100, 20:80, 40:60, 60:40, 80:20, v/v). Plant height, stem diameter, number of leaves, rates of a, b and total chlorophyll, leaf area, root length, shoots and roots dry weight and the Dickson Quality Index were evaluated 90 days after sowing. All three types of residues evaluated showed potential to be used in the elaboration of growth substrates for the production of C. pulcherrima L. Sw. seedlings. The substrates formulated with 33%, 23% or 5% of organic tree pruning + animal manure, urban waste compost and residue of the Agave sisalana fiber extraction, respectively, promoted better quality of seedlings 90 days after sowing, regardless of the soil class.

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Two Heme-Dependent Terminal Oxidases Power Staphylococcus aureus Organ-Specific Colonization of the Vertebrate Host

mBio ◽

10.1128/mbio.00241-13 ◽

2013 ◽

Vol 4 (4) ◽

Cited By ~ 73

Author(s):

Neal D. Hammer ◽

Michelle L. Reniere ◽

James E. Cassat ◽

Yaofang Zhang ◽

Amanda O. Hirsch ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Respiratory Chain ◽

De Novo ◽

Anaerobic Respiration ◽

Systemic Infection ◽

Heme Biosynthesis ◽

Aerobic Respiration ◽

Content Type ◽

Terminal Oxidases ◽

Organ Specific

ABSTRACTStaphylococcus aureusis a significant cause of infections worldwide and is able to utilize aerobic respiration, anaerobic respiration, or fermentation as the means by which it generates the energy needed for proliferation. Aerobic respiration is supported by heme-dependent terminal oxidases that catalyze the final step of aerobic respiration, the reduction of O2to H2O. An inability to respire forces bacteria to generate energy via fermentation, resulting in reduced growth. Elucidating the roles of these energy-generating pathways during colonization of the host could uncover attractive therapeutic targets. Consistent with this idea, we report that inhibiting aerobic respiration by inactivating heme biosynthesis significantly impairs the ability ofS. aureusto colonize the host. Two heme-dependent terminal oxidases support aerobic respiration ofS. aureus, implying that the staphylococcal respiratory chain is branched. Systemic infection withS. aureusmutants limited to a single terminal oxidase results in an organ-specific colonization defect, resulting in reduced bacterial burdens in either the liver or the heart. Finally, inhibition of aerobic respiration can be achieved by exposingS. aureusto noniron heme analogues. These data provide evidence that aerobic respiration plays a major role inS. aureuscolonization of the host and that this energy-generating process is a viable therapeutic target.IMPORTANCEStaphylococcus aureusposes a significant threat to public health as antibiotic-resistant isolates of this pathogen continue to emerge. Our understanding of the energy-generating processes that allowS. aureusto proliferate within the host is incomplete. Host-derived heme is the preferred source of nutrient iron during infection; however,S. aureuscan synthesize hemede novoand use it to facilitate aerobic respiration. We demonstrate thatS. aureusheme biosynthesis powers a branched aerobic respiratory chain composed of two terminal oxidases. The importance of having two terminal oxidases is demonstrated by the finding that each plays an essential role in colonizing distinct organs during systemic infection. Additionally, this process can be targeted by small-molecule heme analogues called noniron protoporphyrins. This study serves to demonstrate that heme biosynthesis supports two terminal oxidases that are required for aerobic respiration and are also essential forS. aureuspathogenesis.

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