Microbiota

# .font170[Ecological Significance of Viruses]

.marco[
.center[.font90[[[<svg style="height:0.8em;top:.04em;position:relative;fill:steelblue;" viewBox="0 0 448 512"><path d="M94.12 315.1c0 25.9-21.16 47.06-47.06 47.06S0 341 0 315.1c0-25.9 21.16-47.06 47.06-47.06h47.06v47.06zm23.72 0c0-25.9 21.16-47.06 47.06-47.06s47.06 21.16 47.06 47.06v117.84c0 25.9-21.16 47.06-47.06 47.06s-47.06-21.16-47.06-47.06V315.1zm47.06-188.98c-25.9 0-47.06-21.16-47.06-47.06S139 32 164.9 32s47.06 21.16 47.06 47.06v47.06H164.9zm0 23.72c25.9 0 47.06 21.16 47.06 47.06s-21.16 47.06-47.06 47.06H47.06C21.16 243.96 0 222.8 0 196.9s21.16-47.06 47.06-47.06H164.9zm188.98 47.06c0-25.9 21.16-47.06 47.06-47.06 25.9 0 47.06 21.16 47.06 47.06s-21.16 47.06-47.06 47.06h-47.06V196.9zm-23.72 0c0 25.9-21.16 47.06-47.06 47.06-25.9 0-47.06-21.16-47.06-47.06V79.06c0-25.9 21.16-47.06 47.06-47.06 25.9 0 47.06 21.16 47.06 47.06V196.9zM283.1 385.88c25.9 0 47.06 21.16 47.06 47.06 0 25.9-21.16 47.06-47.06 47.06-25.9 0-47.06-21.16-47.06-47.06v-47.06h47.06zm0-23.72c-25.9 0-47.06-21.16-47.06-47.06 0-25.9 21.16-47.06 47.06-47.06h117.84c25.9 0 47.06 21.16 47.06 47.06 0 25.9-21.16 47.06-47.06 47.06H283.1z"/></svg>](https://join.slack.com/t/ipma-2020/shared_invite/zt-j9o8ig7k-LN1~U3d6QJztquYbC6iW7w) Slack - <svg style="height:0.8em;top:.04em;position:relative;fill:steelblue;" viewBox="0 0 512 512"><path d="M502.3 190.8c3.9-3.1 9.7-.2 9.7 4.7V400c0 26.5-21.5 48-48 48H48c-26.5 0-48-21.5-48-48V195.6c0-5 5.7-7.8 9.7-4.7 22.4 17.4 52.1 39.5 154.1 113.6 21.1 15.4 56.7 47.8 92.2 47.6 35.7.3 72-32.8 92.3-47.6 102-74.1 131.6-96.3 154-113.7zM256 320c23.2.4 56.6-29.2 73.4-41.4 132.7-96.3 142.8-104.7 173.4-128.7 5.8-4.5 9.2-11.5 9.2-18.9v-19c0-26.5-21.5-48-48-48H48C21.5 64 0 85.5 0 112v19c0 7.4 3.4 14.3 9.2 18.9 30.6 23.9 40.7 32.4 173.4 128.7 16.8 12.2 50.2 41.8 73.4 41.4z"/></svg>](mailto:marco.chiapello@unito.it) marco.chiapello@unito.it]
]
]

???

- Sarò uno dei vostri docenti per il corso "Interazioni tra piante, microrganismi e ambiente"
]
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# Last lesson recap

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<img src="images/lesson5.png" width="450px" style="display: block; margin: auto;" />
 
.center[.black[.fon300[https://bit.ly/2LqAAwX]]]

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.pull-left[
.summaryL3[
1. The plant-associated microbiome can provide benefits to the plant through various direct or indirect mechanisms

1. Disease-suppressive soils are exceptional ecosystems in which crop plants suffer less from specific soil-borne pathogens than expected owing to the activities of other soil microorganisms

1. Induced Systemic Resistance (ISR) is initiated in roots by plant-growth- promoting microbes (PGPM) and leads to resistance priming in distant parts of the plant

1. Correlation is not causation

1. Microorganisms have a role in cooperative or competitive interactions with other members of the microbiome

1. Eco-evolutionary processes can influence the assembly of plant-associated microbiomes

1. How the microbiota can be exploited
]
]

---

.pull-left[
.summaryL3[
1. The plant-associated microbiome can provide benefits to the plant through various direct or indirect mechanisms

1. .opacity10[Disease-suppressive soils are exceptional ecosystems in which crop plants suffer less from specific soil-borne pathogens than expected owing to the activities of other soil microorganisms]

1. .opacity10[Induced Systemic Resistance (ISR) is initiated in roots by plant-growth- promoting microbes (PGPM) and leads to resistance priming in distant parts of the plant]

1. .opacity10[Correlation is not causation]

1. .opacity10[Microorganisms have a role in cooperative or competitive interactions with other members of the microbiome]

1. .opacity10[Eco-evolutionary processes can influence the assembly of plant-associated microbiomes]

1. .opacity10[How the microbiota can be exploited]
]
]

.m0p[
<img src="images/fuctionOverview.png" width="530px" style="display: block; margin: auto;" />
]
]

---

.pull-left[
.summaryL3[
1. .opacity10[The plant-associated microbiome can provide benefits to the plant through various direct or indirect mechanisms]

1. Disease-suppressive soils are exceptional ecosystems in which crop plants suffer less from specific soil-borne pathogens than expected owing to the activities of other soil microorganisms

1. .opacity10[Induced Systemic Resistance (ISR) is initiated in roots by plant-growth- promoting microbes (PGPM) and leads to resistance priming in distant parts of the plant]

1. .opacity10[Correlation is not causation]

1. .opacity10[Microorganisms have a role in cooperative or competitive interactions with other members of the microbiome]

1. .opacity10[Eco-evolutionary processes can influence the assembly of plant-associated microbiomes]

1. .opacity10[How the microbiota can be exploited]
]
]

.pull-right[
 
.m0p[
<img src="images/disease2.png" width="530px" style="display: block; margin: auto;" />
]
]

---

.pull-left[
.summaryL3[
1. .opacity10[The plant-associated microbiome can provide benefits to the plant through various direct or indirect mechanisms]

1. Induced Systemic Resistance (ISR) is initiated in roots by plant-growth- promoting microbes (PGPM) and leads to resistance priming in distant parts of the plant

1. .opacity10[Correlation is not causation]

1. .opacity10[Microorganisms have a role in cooperative or competitive interactions with other members of the microbiome]

1. .opacity10[Eco-evolutionary processes can influence the assembly of plant-associated microbiomes]

1. .opacity10[How the microbiota can be exploited]
]
]

.pull-right[
.m0p[
<img src="images/disease1.png" width="530px" style="display: block; margin: auto;" />
]
]

---

.pull-left[
.summaryL3[
1. .opacity10[The plant-associated microbiome can provide benefits to the plant through various direct or indirect mechanisms]

1. .opacity10[Induced Systemic Resistance (ISR) is initiated in roots by plant-growth- promoting microbes (PGPM) and leads to resistance priming in distant parts of the plant]

1. Correlation is not causation

1. .opacity10[Microorganisms have a role in cooperative or competitive interactions with other members of the microbiome]

1. .opacity10[Eco-evolutionary processes can influence the assembly of plant-associated microbiomes]

1. .opacity10[How the microbiota can be exploited]
]
]

.pull-right[
 
.m0p[
<img src="images/shape5.png" width="530px" style="display: block; margin: auto;" />
]
]

---

.pull-left[
.summaryL3[
1. .opacity10[The plant-associated microbiome can provide benefits to the plant through various direct or indirect mechanisms]

1. .opacity10[Induced Systemic Resistance (ISR) is initiated in roots by plant-growth- promoting microbes (PGPM) and leads to resistance priming in distant parts of the plant]

1. .opacity10[Correlation is not causation]

1. Microorganisms have a role in cooperative or competitive interactions with other members of the microbiome

1. .opacity10[Eco-evolutionary processes can influence the assembly of plant-associated microbiomes]

1. .opacity10[How the microbiota can be exploited]
]
]

.pull-right[
 
.m0p[
<img src="images/shape9.png" width="530px" style="display: block; margin: auto;" />
]
]

---

.pull-left[
.summaryL3[
1. .opacity10[The plant-associated microbiome can provide benefits to the plant through various direct or indirect mechanisms]

1. .opacity10[Induced Systemic Resistance (ISR) is initiated in roots by plant-growth- promoting microbes (PGPM) and leads to resistance priming in distant parts of the plant]

1. .opacity10[Correlation is not causation]

1. .opacity10[Microorganisms have a role in cooperative or competitive interactions with other members of the microbiome]

1. Eco-evolutionary processes can influence the assembly of plant-associated microbiomes

1. .opacity10[How the microbiota can be exploited]
]
]

.pull-right[
 
.m0p[
<img src="images/ecoevo1.png" width="280px" style="display: block; margin: auto;" />
]
]

---

.pull-left[
.summaryL3[
1. .opacity10[The plant-associated microbiome can provide benefits to the plant through various direct or indirect mechanisms]

1. .opacity10[Induced Systemic Resistance (ISR) is initiated in roots by plant-growth- promoting microbes (PGPM) and leads to resistance priming in distant parts of the plant]

1. .opacity10[Correlation is not causation]

1. .opacity10[Microorganisms have a role in cooperative or competitive interactions with other members of the microbiome]

1. .opacity10[Eco-evolutionary processes can influence the assembly of plant-associated microbiomes]

1. How the microbiota can be exploited
]
]

.pull-right[
 
.m0p[
<img src="images/bioc3.png" width="580px" style="display: block; margin: auto;" />
]
]

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# Virus short surveys

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# What is a Virus?

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???

- In base a studi sierologici la maggior parte di noi è infetta da herpes

- Dell'herpes non puoi liberarti

- A differenza dell'amore, un herpes virus e per sempre
]

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- We regularly eat and breathe billions of viral particles

- We carry viral genomes as part of our own genetic material
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]

.pull-right[
.m0tbp[
<img src="images/vir4.png" width="400px" style="display: block; margin: auto;" />
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- In the world's waters (salt water) there are 1030 bacteriophage (viruses that infect bacteria) particles

- 10'000'000'000'000'000'000'000'000'000'000
 
- A bacteriophage particle weight about a femtogram (10-15 grams)

- <svg style="height:0.8em;top:.04em;position:relative;fill:red;" viewBox="0 0 192 512"><path d="M176 432c0 44.112-35.888 80-80 80s-80-35.888-80-80 35.888-80 80-80 80 35.888 80 80zM25.26 25.199l13.6 272C39.499 309.972 50.041 320 62.83 320h66.34c12.789 0 23.331-10.028 23.97-22.801l13.6-272C167.425 11.49 156.496 0 142.77 0H49.23C35.504 0 24.575 11.49 25.26 25.199z"/></svg> 1030 X 10-15 = biomass on the oceans of the bacteriophages. This exceeds the biomass of elephants by more than 1000-fold!

- The length of a head to tail line of 1030 phages is 100 millions light years!
]
]
]

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- The human virome is the total collection of viruses in and on the human body

- Some viruses cause disease, while others may be asymptomatic or just pass by

- There are roughly 40 trillion bacteria in a typical human microbiome, and generally virions outnumber bacteria 10:1 in nature
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]
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.pull-right[
.m0tp[
<img src="images/vir5.png" width="400px" style="display: block; margin: auto;" />
]]

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???

- 1.5% rappresenta i coding genes

- Osservate i LTR retrotransposons (possiedono alle estremità sequenze ripetute dalle 100 alle 5000 bp). Una buona parte di loro derivano da infezzioni da retrovirus che sono successe molto prima che noi fossimo *homo sapiens*

- Alcuni di quei geni sono ad oggi utilizzati dagli esseri umani
]

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???

- Virus coinvolti in molte malatti e cause di morte => studiati

- Ma sempre più stiamo capendo e studiando il ruolo che i virus hanno negli ecosistemi e i loro ruoli benefici
]

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- We ingest many non-animal viruses regularly with foods
 - Cabbage from 5 different supermarkets in Washington D.C.
 - Each serving (~100 cm2 of leaf material) would contain up to 108 particles of virus pathogenic for the cabbage looper (caterpiller)

- Study on human feces:
 - Most RNA virus sequences (91%) were similar to plant virus
 - Most abundant human fecal virus: pepper mild mottle virus (109 virions per gram of dry feces)

]
]
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.pull-right[
.limg[
<img src="images/vir8.png" width="300px" style="display: block; margin: auto;" />
<img src="images/vir9.png" width="120px" style="display: block; margin: auto;" />
]
<img src="images/vir10.png" width="130px" style="display: block; margin: auto;" />
]

???

- Se siete interessati ci sono aziende che studiano la composizione virale delle vostre feci
]

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???

.n30[
- Polyomavirus infetta chiunque, lo si prende nei primi mesi di vita dai famigliari e lo si ha per tutta la vita

- Di solito non causa sintomi a meno che il soggetto non sia immunodepresso

- Puo' essere usato, vista la loro diffusione, per tracciare gli spostamenti delle popolazioni (migrazioni)

- Linea tratteggiata e' la migrazione dell'h. sapiens studiata grazie al sequenziamento dei genomi umani

- Linea nera e' la migrazione dell'h. sapiens studiata grazie al Polyomavirus (differenti lineages hanno diversi polyomavirus)

- Polyomavirus da maggiori dettagli che lo studio del genoma

- Polyomavirus
]

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- A virus is a submicroscopic **infectious** agent that replicates its **genetic material** (DNA or **RNA**) only inside the living cells of an organism (**obligate intracellular parasites**)

- Viruses are often surrounded by a protein coat, somethime a membrane

- Viruses **use the host's cells to replicate** by forcing it to rapidly produce thousands of identical copies of the original virus

- When not inside the host, viruses **exist in the form of independent particles** (virions)

]
]]

???

- Se non hanno un ospite non possono replicarsi

- i virus non si riproducono per fissazione, ma per assemblaggio di parti
]
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- Viruses **can't capture or store any energy**, so they **rely on the cells of other organisms** to survive and reproduce

- They can not function outside a host organism! Owing on that they are often **regarded as non-living** 
 
- On the other hand they **carry genetic material**, **reproduce**, and **evolve** through natural selection

- Viruses are considered by some biologists to be a life form

- Vviruses have been described as "**organisms at the edge of life**"

]
]
]

.pull-right[
.m0tbp[
<img src="images/vir12.png" width="250px" style="display: block; margin: auto;" />
<img src="images/vir13.png" width="250px" style="display: block; margin: auto;" />
]]

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layout: false

.content-box-grey4[
Viruses do NOT think 
They do not achieve their goal in a human-centered manner 
**Viruses are passive agents**
]

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.h25up[
- Ecological Significance of Viruses <img src="images/virus-3128.png" style="height:1em; width:auto; "/> 
 - Ecological Importance of Viruses in the Oceans
 - Endogenous Virus Elements and Beneficial Infection in Vertebrates
 - Mycovirus involved in mutualistic symbiosis

]
]

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# .black[Ecological Importance of Viruses in the Oceans]

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layout: true

# Ecological Importance of Viruses in the Oceans

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- The oceans cover **more than 70%** of the Earth’s surface

- They control the **climate**, provide a significant amount of the **protein** that is consumed globally and produce approximately **half of the Earth’s oxygen**

- Microorganisms are a major force behind the **nutrient and energy cycles** in the world’s oceans

- It is estimated that **viruses kill approximately 20% of this biomass per day**

- As well as being agents of mortality, viruses are one of the **largest reservoirs of unexplored genetic diversity** on the Earth.
]
]
]

.pull-right[
.m0tp[
<img src="images/vir18.png" width="400px" style="display: block; margin: auto;" />
]
]

???

- Hanno funzioni ed effetti che si ripercuotono sul genere umano:
  - Clima
  - Provvedono alla produzione di circa la metù dell'ossigeno 
  - Dal pesce si produce circa la metà delle proteine consumate globalmente

- I microorganismi sono la principale forza dietro il ciclo  energetico degli oceani

- E questi stessi microorganismi sono sono uccisi dai virus presenti nei mari. Si stima che circa il 20% della biomassa dei microorganismi marini sia uccisa ogni giorno dai virus

- D'altro canto i virus sono un'enorme fonte, inesplorata, di biodiversitù
]

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- **Virosphere** is the portion of the Earth in which viruses occur or which is affected by viruses

- The virosphere is inclusive of **every environment on the Earth**, from the atmosphere to the deep biosphere

- Nowhere is the importance of viruses more evident than in the world’s oceans

- Viruses are substantial **agents of mortality** in heterotrophic and autotrophic plankton

- Viruses are major players in the mortality of marine microorganisms and, consequently, **affect nutrient and energy cycles** as well as the structure of microbial communities

- Need to incorporate viruses and virus-mediated processes into our understanding of **ocean biology** and biogeochemistry
]
]
]

???

- Gli oceani sono sicuramente una virisfera in cui i virus hanno un'importanza ecologica fondamentale

- Essi sono sostanzialmente agenti di mortalità e quindi hanno profondi effetti sul ciclo dei nutrienti e energetico. Nonchè sulla vita/morte di molti microorganismi

- I biologi marini stanno studiando sempre di più i virus e la loro importanza nei mari
]

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- The abundance of viruses in oceans exceeds that of bacteria and archaea by approximately 15-fold and comprising approximately **94% of the nucleic-acid-containing particles**

- However, because of their extremely small size, viruses represent only approximately **5% of the biomass**

- In the oceans, viral abundance decreases further offshore and deeper in the water column because it generally **varies along with the prokaryotic abundance**
]
]
]

.pull-right[
 
<img src="images/vir15.png" width="540px" style="display: block; margin: auto;" />
.right[.font50[(Suttle, 2007)]]
]

???

- Ma essendo molto piccoli rappresentano solo il 5% della biomassa marinao

- La loro abbondanza si correla con l'abbondanza degli altri microorganismi
]

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- Six methods are used to estimate the abundance of viruses in aquatic samples
  - plaque assays (PAs) and most-probable-number assays (MPNs): are used to quantify the abundance of infectious units that cause the lysis of a particular host.
  - transmission electron microscopy (TEM): TEM is the only method that provides data on both the abundance and morphology of virus-like particles (fig a)
  - **epifluorescence microscopy** (EfM): the viruses are concentrated on a membrane filter, their nucleic acids are stained with a brightly fluorescent dye and the abundance of viruses is estimated (fig b)
  - flow cytometry (FC): accurate high-throughput method also allows the quantification of subpopulations of viruses
  - **Next generation sequencing**
]
]

.pull-right[
<img src="images/vir20.png" width="300px" style="display: block; margin: auto;" />
.right[.font50[(Suttle, 2007)]]
]

???

- Ci sono almeno 6 diverse metodologie

- Vorrei citarne 3:
  1. TEM: molto precisa e l'unica a dare informazioni sia su abbondanza e morfologia
  1. Epifluorescenza: molto precisa nella stima dell'abbondanza dei virus. 
  1. NGS (HT)
]

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- As agents of mortality, viruses have a range of effects on the world’s oceans, from altering geochemical cycles to structuring populations and communities.

- 20-40% of prokaryotes in surface water are removed by viruses every day (similar to the amount killed by grazing)
  
- Increase in the rate of viral reproduction in response to an increase in the growth rate of host cells is a strong feedback mechanism that would probably prevent dominance by the fastest growing taxa

]

???

.h202[
- Vi riporto qui una figura che schematizza l'importanza dell'interazione tra virus e microorganismi marini

- Potete osservare la complessitù di queste interazioni

- E capire come i virus possano avere effetti sulla struttura delle comunità, sul ciclo dei nutrienti e sulla proliferazione di determinate specie
]

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- **Viral shunt**: the viral-mediated movement of nutrients from organisms to pools of dissolved and non-living particulate organic matter

- The viral shunt moves material from living organisms into **particulate organic matter** (POM) and **dissolved organic matter** (DOM)

- However, the effects can also be more profound and potentially include:
  - the **release of dimethyl sulphide**, a gas that affects the Earth’s climate
  - the **remobilization of the organically complexed iron** that limits primary production in much of the world’s oceans (for example, the viral lysis of prokaryotes liberates sufficient amounts of biologically available iron to support the needs of phytoplankton)
]
]
]

.pull-right[
 
<img src="images/vir16.png" width="500px" style="display: block; margin: auto;" />
.right[.font50[(Suttle, 2007)]]
]

???

- Il viral shunt è definito come il movimento mediato dai virus di materia organica dei micororganismi a materia organica dissolta o particolata

- In particolare possiamo definire 2 prodotti del viral shunt
  1. POM: particulate organic matter, coinvolto nella pompa biologica
  1. DOM: dissolved organic matter

- Oltre alla produzione di POM e DOM ci sono altri effetti, per esempio:
  1. Il rilascio di Dimethyl sulphide, un gas che è coinvolto nel clima terrestre
  1. La rimobilitazione del ferro. Pensate che il ferro rilasciato in mare dalla lisi dei procarioti è sufficiente per i bisogni del phytoplankton
]

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- DOM, the **largest reservoir of carbon in the oceans**, is only available for uptake by bacteria

- There are **two main forms of bacterial mortality**: predation by unicellular eukaryotic grazers or lysis by phages
  - **Grazing** moves carbon up through the trophic levels from bacteria to protozoa to zooplankton to fish and larger organisms
  - When bacteria are **lysed by phages**, carbon and nutrients flow through the viral shunt and are remineralized by bacteria within the microbial loop, making the viral shunt function as the ocean’s recycling system
]
]
]

.pull-rigth[
 
<img src="images/vir23.png" width="550px" style="display: block; margin: auto;" />
.right[.font50[(Breitbart, Bonnain, Malki, and Sawaya, 2018)]]
]

???

.h202[
- La dissolved organic matter è la più grande riserva di carbonio degli oceani ed è utilizzata dai batteri

- Ci sono 2 forme di mortalità batterica:
 1. Il "pascolo" (grazing) che muove il carbonio a livelli trofici più alti
 1. Viral shunt che fa ritornare il carboni dei batteri a DOM

]

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- The biological pump (BP) is a combination of processes that leads to the sequestration of carbon in the deep ocean as the result of the sinking of **PoM** from surface waters

- The amount of carbon that is exported by the BP has direct implications for the concentration of carbon dioxide in the atmosphere

- Carbon from cell lysis will sink more slowly and be retained to a greater extent in surface waters, where much of it will be converted to dissolved inorganic carbon by respiration or solar radiation

]
]
]

.pull-rigth[
 
<img src="images/vir23.png" width="550px" style="display: block; margin: auto;" />
.right[.font50[(Breitbart Bonnain, et al., 2018)]]
]

???

- La BP è una combinazioni di processi che conduce alla precipitazione del carbinio nelle profondità degli oceani

- È stato studiato che il carbonio esportato dalla PB ha effetto sulle concentrazioni di anidride carbonica nell'atmosfera
]

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**Viruses manipulate the marine environment**
.pull-left[
.m0tp[
.par25[

- Until now we focused on two areas:
  - **viruses as pathogens** of aquatic organisms
  - **virus-driven dynamics** of the marine microbial food web

- Marine viruses can affect their hosts and environments in startling ways:
  - **Global transfer** of niche adaptation genes
  - Modifications of the **ontogeny and ecology** of marine organisms

**It has become clear that the marine virome is a master of manipulation**
]
]
]

.pull-rigth[
<img src="images/vir24.png" width="500px" style="display: block; margin: auto;" />
.right[.font50[(Rohwer and Thurber, 2009)]]
]

???

.h202[
- Riassumento quanto visto finora, ci siamo concentrati su 2 aree:
  1. I virus come patogeni
  1. I virus come componente integrante della nutrizione marina

- I virus possono avere anche altri effetti :
  1. Il trasferimento di geni all'ospite
  1. La modificazione dell'ecologia marina
]

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**Virally encoded host genes**
.pull-left[
.m0tp[
.par25[

- Phage are known to carry and **transfer a variety of host genes**

- Most studies of this phenomenon have focused on the negative effects, but **viral infections can augment the metabolism, immunity, distribution and evolution of their hosts** in many unexpected and potentially positive ways

]
]
]

.pull-rigth[
<img src="images/vir24.png" width="500px" style="display: block; margin: auto;" />
.right[.font50[(Rohwer and Thurber, 2009)]]
]

???

- Questi geni possono anche essere trasferiti o espressi dal fago per alterare il metabolismo dell'ospite

- Quasi tutti gli studi su questo fenomeno hanno studiato gli effetti negativi, ma l'infezione virale puà anche avere effetti positivi: come aumentare metabolismo, immunità, distribuzione ed evoluzione dell'ospite in modi inaspettati
]

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**Virally encoded host genes**
.pull-left[
*Accessory gene expression*
.m0tp[
.par20[

- Consider the **cyanobacteria**l which together account for about 25% of global photosynthesis

- Sequencing of the marine viral **cyanophage**s that infect these primary producers showed that **genes involved in photosynthesis** are commonly carried in phage genome

- During the lytic cycle, most of the host’s transcription and translation is **shut down by phage**

- By expressing genes involved in photosynthesis, **phage generate the energy necessary for viral production**

]
]
]

.pull-rigth[
<img src="images/vir24.png" width="500px" style="display: block; margin: auto;" />
.right[.font50[(Rohwer and Thurber, 2009)]]
]

???

.h202[
- È stato studiato il viroma dei cyano batteri che contribuiscono al 25% della fotosintesi globale

- All'interno dei cyanophagi identificati sono stati trovati geni dell'ospite coinvolti nella fotosintesi

- Durante la fase litica dell'infezione virale, trascrizione e traslazione sono inattivate

- Il virus quindi esprime geni coinvolti nella fotosintesi per aiutare l'ospite a generare l'energia necessaria per la sua replicazione
]

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**Virally encoded host genes**
.pull-left[
*Horizontal gene transfer*
.m0tp[
.par20[

- One consequence of cyanophage carrying genes involved in the photosynthesis is the **horizontal gene transfer of photosynthetic genetic elements** between hosts

- Specific ecotypes that live in different parts of the water column and are **tuned to the different light and nutrient regimes**

- Given the prevalence of phage-encoded photosynthesis proteins and the occurrence of recombination between phage and host genes, phage populations are expected to **serve as gene reservoirs**

]
]
]

.pull-rigth[
<img src="images/vir24.png" width="500px" style="display: block; margin: auto;" />
.right[.font50[(Rohwer and Thurber, 2009)]]
]

???

- Phagi e ospite possono ricombinare e quindi puù avvenire il trasferimento orizzontale di geni

- I phagi possono essere quindi considerati come una riserva di geni per i loro ospiti
]

---
class: clear, middle, center

# .black[Endogenous Virus Elements]

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---
layout: true

# Endogenous Virus Elements

---

- An endogenous viral element (**EVE**) is a viral DNA sequence, present within the germline of a non-viral organism

- EVE may be entire viral genome or a fragment of viral genome

- EVEs are **usually eliminated** from the host gene pool within a small number of generations, but they can sometimes **reach fixation**

- EVEs that occur as **proviruses** can potentially remain capable of **producing infectious virus** 
]
]
]

.pull-right[
<img src="images/vir25.png" width="px" style="display: block; margin: auto;" />
.right[
.parR[
.font50[By Adrian.maglaqui - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=48727769]]
]]

???

.h202[
- Gli elementi endogenizzati virali (EVE), sono sequenze di genoma virale presenti bel genoma dell'ospite

- Questi elementi possono essere l'intero genoma virale o anche solo frammenti

- Di solito i meccanismi di protezione dell'ospite eliminano queste intregrazioni ma alcune volte esse vendono fissate e rimango nel genoma dell'ospite

- Una cosa estremamente interessante è che se il genoma virale viene fissato interamente puà rimanere in grado di produrre infezioni virali
]

---

- Endogenous retroviruses are a **common ancestral feature of mammalian genomes** with most having been inactivated over time through mutation and deletion

- Koala retrovirus (**KoRV**) is associated with koala neoplasia

- KoRV also shows features of a recently inserted endogenous retrovirus that is vertically transmitted

- **Isolated koala populations** have not yet incorporated KoRV into their genomes suggesting that KoRV is a **virus in transition** between an exogenous and endogenous element

- Opportunity to study the process and consequences of retroviral endogenization in action
]
]
]

.pull-right[
 
<img src="images/vir26.png" width="450px" style="display: block; margin: auto;" />
.right[.font50[(Tarlinton, Meers, and Young, 2006)]]
]

???

- I retrovirus endogenizzati sono, come abbiamo visto parte integrante del genoma dei mammiferi e la maggior parte di essi è inattiva

- Un retrovirus di Koala è associato ad un tumore del koala

- Recenti studi hanno dimostrato l'inserzione di questo retrovirus nel genoma del koala e di conseguenza la sua trasmissione verticale (da madre a figlio)

- In Australia ci sono popolazioni isolate di Koala che non hanno ancora incorporato il virus come parte del loro genoma

- Per i ricercatori questo processo è estremamente interessante perchè si possono studiare il processo e le conseguenze dell'endogenizzazione durante il suo svolgimento 
]

---

.pull-left[
**Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis**
.m0tp[
.par20[

- Example of a viral gene that has been sequestered to serve an important function in the physiology of a mammalian host

- This gene, encoding a protein that we have called **syncytin**, is the envelope gene of a recently identified **human endogenous defective retrovirus**, HERV-W

- Data indicate that syncytin may be important in **human placental morphogenesis**

- **Syncytin disregulation or dysfunction** is involved in pathologies such as preeclampsia or choriocarcinoma is a focus of ongoing studies

]
]
]

.pull-right[
<img src="images/syn1.jpg" width="450px" style="display: block; margin: auto;" />
.right[.font50[(Mi, Lee, Li, Veldman, Finnerty, Racie, LaVallie, Tang, Edouard, Howes, Keith, and McCoy, 2000)]]
]

???

.h202[
- Un altro esempio molto interessante è quello della proteina syncytin la cui funzione è stata utilizzata dall'ospite (uomo) per una sua specifica funzione fisiologica

- integration likely occurred more than 25 million years ago

- Questa proteina del virus chiamato HERV, serve alla produzione dell'envelope del virus

- Mentre nell'uomo questa proteina è fondamentale per la morfogenesi della placenta

- La disfunzione di questo gene causa gravi problemi come la preclamsia
]

---

.pull-left[
**Endogenous retroviral sequences are required for tissue-specific expression of a human salivary amylase gene**
.m0tp[
.par20[

- The human genome contains three salivary and two pancreatic amylase genes

- The three **salivary amylase genes** are each associated with an **intact retroviral element**

- The two **pancreatic amylase genes** either lack retroviral sequences (AMY2B) or contain a solo LTR as a result of excision of the retrovirus (AMY2A).

- The gene structures are consistent with a sequence of events in which **insertion of the retrovirus converted a pancreatic amylase gene like AMY2B into a salivary-specific gene**, and excision of the retrovirus resulted in a return to pancreas-specific expression of AMY2A.

]
]
]

.pull-right[
 
<img src="images/end1.png" width="450px" style="display: block; margin: auto;" />
.right[.font50[(Ting, Rosenberg, Snow, Samuelson, and Meisler, 1992)]]
]

???

- Le tre amilasi salivari sono associate con elementi retroviali

- In particolare è stato dimostrato che l'inserzione retrovirale ha modificato le amilasi pancreatiche in amilasi salivari

- Esperimenti di rimozione dell'inserzione retrovirale hanno riconvertito le amilasi salivari a pancreatiche

]

---

.pull-left[
**An enteric virus can replace the beneficial function of commensal bacteria**
.m0tp[
.par20[

- The symbiotic contribution on host physiology of **commensal bacteria is well established**

- The **role of eukaryotic viruses** that are present in the gastrointestinal tract under homeostatic conditions is undefined

- Researched demonstrate that a common enteric RNA **virus can replace the beneficial function of commensal bacteria** in the intetine

- Murine norovirus (MNV) infection of germ-free or antibiotic- treated mice **restored intestinal morphology** and **lymphocyte function** without inducing overt inflammation and disease
]
]
]

.pull-right[
<img src="images/noro1.png" width="450px" style="display: block; margin: auto;" />
<img src="images/noro2.png" width="450px" style="display: block; margin: auto;" />
.right[.font50[(Kernbauer, Ding, and Cadwell, 2014)]]
]

???

.h202[
- Vediamo un esempio in cui un virus puà aiutare il suo ospite quando il suo microbiota intestinale è distrutto

- Il Murine norovirus è in grado di ripristinare la morfologia intestinale senza indurre infiammazioni o malattia
]

---
class: clear, middle, center

# .black[Mycovirus involved in mutualistic symbiosis]

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---
layout: true

# Mycovirus involved in mutualistic symbiosis

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- Discovered in 1962

- As most viruses not phylogenetically homogeneous. Different evolutionary trajectories

- Mostly dsRNA...but also  ssRNA, and recently -ssDNA

- Often the result of long co-evolution. Neutral or beneficial symbiosis

]
]
]

.pull-right[
<img src="images/myco1.jpg" width="350px" style="display: block; margin: auto;" />
.right[.font50[(Kotta-Loizou and Coutts, 2017)]]

]

???

- Sono stati scoperti recentemente

- Non presentano una filogenesi comune

- Sono principalmente dsRNA, ma esisto anche ssRNA e ssDNA

- Questi virus spesso non hanno effetti sul loro ospite o addirittura hanno effetti benefici. Questo dovuto alla lunga co-evoluzione
]

---

- Extracellular transmission was excluded until recent years

- **Vertically**: during sporogenesis: asco, basidio, and conidio spores have different efficiency of transmission according to the specific virus-host interaction

- **Horizontally**: regulated by vegetative compatibility groups (VC)

]
]
]

.pull-right[
 
<img src="images/myco2.png" width="550px" style="display: block; margin: auto;" />
.right[.font50[(Nuss, 2005)]]

]

???

.h202[
- I micovirus si trasmettono in 2 modi
  1. Vericalmente: durante la produzione di spore. Il virus viene trasmesso quindi alla progenie, anche se con diverse efficienze a seconda della specie fungina
  1. Orizzontalmente: tramite anastomosi
]

---

**Mycovirus biodiversity**

<img src="images/myco3.png" width="850px" style="display: block; margin: auto;" />
.right[.font50[(Nuss, 2005)]]

???

.h202[
- Vedete qui un albero filogenetico dei micovirus e delle 5 branch in cui è separato secondo l'ICTV (International Committee on Taxonomy of Viruses)
]

---

.pull-left[
**A Virus in a Fungus in a Plant: Three-Way Symbiosis Required for Thermal Tolerance**
.m0tp[
.h202[

- A mutualistic association between a fungal endophyte and a tropical panic grass allows both organisms to grow at high soil temperatures

- **Fungal isolates cured of the virus are unable to confer heat tolerance**, but heat tolerance is restored after the virus is reintroduced

- The virus-infected fungus **confers heat tolerance not only to its native monocot host but also to a eudicot host**, which suggests that the underlying mechanism involves pathways conserved between these two groups of plants
]
]
]

.pull-right[
<img src="images/myco4.png" width="450px" style="display: block; margin: auto;" />
<img src="images/myco5.png" width="450px" style="display: block; margin: auto;" />
.right[.font50[(Márquez, Redman, Rodriguez, and Roossinck, 2007)]]

]

???

- So che ve ne ha già parlato la prof. Perotto, quindi ...

]

---

**A Virus in a Fungus in a Plant: Three-Way Symbiosis Required for Thermal Tolerance**

.pull-right[
<img src="images/myco7.png" width="450px" style="display: block; margin: auto;" />
.right[.font50[(Márquez Redman, et al., 2007)]]

]

---

# Questions about the lesson

---

.m0tbp[
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]