layout: true --- name: xaringan-title class: center, bottom, inverse background-color: #1F4E74 background-image: url(img/panama_dna_50.png) font-color: white background-size: contain background-position: center # Rethinking the Diversity of Life <!-- <img src="https://user-images.githubusercontent.com/163582/45438104-ea200600-b67b-11e8-80fa-d9f2a99a03b0.png" alt="Sharingan" width="180" />--> ### .fancy[A conceptual tour of the microbial world] by Jarrod J Scott | STRI | Panama <!-- this ends up being the title slide since seal = FALSE--> [Credits](#credits) Source Code [<svg style="height:0.8em;top:.04em;position:relative;" viewBox="0 0 496 512"><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>](https://github.com/istmobiome/istmobiome.github.io/tree/master/rethink-d) --- name: background class: left, top background-image: url(img/land.jpg) <!-- background-size: cover--> ### A little about your tour guide --- name: overview class: center, middle ## Connectivity of Systems ## Magnitude of Diversity ## Uniformity of Forms ### /ʃaː.'riŋ.ɡan/ --- name: connect-intro class: inverse, center, middle ## Connectivity of Systems --- name: iron class: left, right .pull-left[ .microbe-dk[Ancient Rock Art (British Columbia)]  ] .pull-right[ .microbe-dk[Deep-sea Hydrothermal Vent (Mariana Back Arc)]  ] --- name: mag-intro class: inverse, center, middle ## Magnitude of Diversity --- name: magnitude class: middle background-image: url(img/life_tree.jpg) background-size: contain background-position: center --- name: mag-intro class: inverse, center, middle ## Variety of Forms --- name: forms background-color: #000000 class: middle .pull-left[ .microbe-lt[Abundant & Familiar Forms]  ] -- .pull-right[ .microbe-lt[Limited & Uninformative Forms]  ] --- name: library class: inverse, center, middle ### An Ecosystem is a Library of Genomes .microbe-lt[and we want to read all the books]  ] --- name: genome_book class: inverse, center, middle  --- name: workflow class: middle ### From there to here... .microbe-big-dk[Metagenomics as a tool to explore hidden microbial dimensions across the Isthmus of Panama] <div id="htmlwidget-55696658c217ca839e50" style="width:100%;height:25%;" class="grViz html-widget"></div> <script type="application/json" data-for="htmlwidget-55696658c217ca839e50">{"x":{"diagram":"digraph {\n\ngraph [layout = \"dot\",\n outputorder = \"edgesfirst\",\n bgcolor = \"white\",\n rankdir = \"LR\"]\n\nnode [fontname = \"Helvetica\",\n fontsize = \"10\",\n shape = \"circle\",\n fixedsize = \"true\",\n width = \"0.5\",\n style = \"filled\",\n fillcolor = \"aliceblue\",\n color = \"gray70\",\n fontcolor = \"gray50\"]\n\nedge [fontname = \"Helvetica\",\n fontsize = \"8\",\n len = \"1.5\",\n color = \"gray80\",\n arrowsize = \"0.5\"]\n\n \"1\" [label = \"Field\", shape = \"rectangle\", color = \"#3C3C3C\", fontname = \"Lato\", fontcolor = \"black\", width = \"1.2\", fillcolor = \"#61acf0\"] \n \"2\" [label = \"Lab\", shape = \"rectangle\", color = \"#3C3C3C\", fontname = \"Lato\", fontcolor = \"black\", width = \"1.2\", fillcolor = \"#E69F00\"] \n \"3\" [label = \"Computer\", shape = \"rectangle\", color = \"#3C3C3C\", fontname = \"Lato\", fontcolor = \"black\", width = \"1.2\", fillcolor = \"#CC79A7\"] \n\"1\"->\"2\" [color = \"#3C3C3C\"] \n\"2\"->\"3\" [color = \"#3C3C3C\"] \n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script> <div id="htmlwidget-71291bc3d32ee62b7298" style="width:100%;height:25%;" class="grViz html-widget"></div> <script type="application/json" data-for="htmlwidget-71291bc3d32ee62b7298">{"x":{"diagram":"digraph {\n\ngraph [layout = \"dot\",\n outputorder = \"edgesfirst\",\n bgcolor = \"white\",\n rankdir = \"LR\"]\n\nnode [fontname = \"Helvetica\",\n fontsize = \"10\",\n shape = \"circle\",\n fixedsize = \"true\",\n width = \"0.5\",\n style = \"filled\",\n fillcolor = \"aliceblue\",\n color = \"gray70\",\n fontcolor = \"gray50\"]\n\nedge [fontname = \"Helvetica\",\n fontsize = \"8\",\n len = \"1.5\",\n color = \"gray80\",\n arrowsize = \"0.5\"]\n\n \"1\" [label = \"1. Collect\\n Samples\", shape = \"circle\", color = \"#3C3C3C\", fontname = \"Lato\", fontcolor = \"black\", width = \"1\", fillcolor = \"#61acf0\"] \n \"2\" [label = \"2. Filter\\n Samples\", shape = \"circle\", color = \"#3C3C3C\", fontname = \"Lato\", fontcolor = \"black\", width = \"1\", fillcolor = \"#61acf0\"] \n \"3\" [label = \"3. Extract\\n the DNA\", shape = \"circle\", color = \"#3C3C3C\", fontname = \"Lato\", fontcolor = \"black\", width = \"1\", fillcolor = \"#E69F00\"] \n \"4\" [label = \"4. Read\\n the DNA\", shape = \"circle\", color = \"#3C3C3C\", fontname = \"Lato\", fontcolor = \"black\", width = \"1\", fillcolor = \"#E69F00\"] \n \"5\" [label = \"5. Assemble\\n the DNA\", shape = \"circle\", color = \"#3C3C3C\", fontname = \"Lato\", fontcolor = \"black\", width = \"1\", fillcolor = \"#CC79A7\"] \n \"6\" [label = \"6. Rebuild\\n Genomes\", shape = \"circle\", color = \"#3C3C3C\", fontname = \"Lato\", fontcolor = \"black\", width = \"1\", fillcolor = \"#CC79A7\"] \n\"1\"->\"2\" [color = \"#3C3C3C\"] \n\"2\"->\"3\" [color = \"#3C3C3C\"] \n\"3\"->\"4\" [color = \"#3C3C3C\"] \n\"4\"->\"5\" [color = \"#3C3C3C\"] \n\"5\"->\"6\" [color = \"#3C3C3C\"] \n}","config":{"engine":"dot","options":null}},"evals":[],"jsHooks":[]}</script> --- name: collecting class: inverse, center, middle ### N^<u>o</u>1 Collect samples .pull-left[ .microbe-lt[Coral Reef Habitat]  ] .pull-right[ .microbe-lt[Mangrove Habitat]  ] --- name: filtering class: inverse, center, middle ### N^<u>o</u>2 Filter samples .pull-left[ .microbe-lt[Pour]  ] .pull-right[ .microbe-lt[...and Drill]  ] --- name: shred class: inverse, center, middle ### N^<u>o</u>3 Extract & N^<u>o</u>4 Read the DNA .pull-left[  ] .pull-left[  ] --- name: dag class: center, middle ### N^<u>o</u>5 Assemble the DNA & N^<u>o</u>6 Rebuild Genomes  --- name: chaos background-color: #FFFFFF class: middle, split-four .column[ <img src="img/otu_EBB1.png"> Loihi Seamount <img src="img/otu9_SV108.png"> Mariana Back Arc Basin ] .column[ <img src="img/otu11_M34.png"> Loihi Seamount <img src="img/otu9_TAG1.png"> Mid-Atlantic Ridge ] .microbe-dk[Chaos Game <br/> Maps] --- name: mag-intro class: inverse, center, middle ### Emergent Self-Organizing Map  --- name: end class: center, middle, inverse background-color: #1F4E74 background-image: url(img/panama_dna_50.png) font-color: white background-size: contain background-position: center # Rethinking the Diversity of Panama --- name: credits class: left, middle background-color: #F2F2F2 font-color: #191919 background-size: contain background-position: center # Credits & Resources * Find the source code for the presentation here [<svg style="height:0.8em;top:.04em;position:relative;" viewBox="0 0 496 512"><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>](https://github.com/istmobiome/istmobiome.github.io/tree/master/rethink-d). * Slides created with the R package [xaringan](https://github.com/yihui/xaringan). * [Title slide](#aringan-title) designed by the author. * [Leaf-cutter ant](#background) photo by the author. * Image on left of [ancient rock art](#iron) from MacDonald, et al. *Hunter-Gatherers Harvested and Heated Microbial Biogenic Iron Oxides to Produce Rock Art Pigment*. (2019) [Scientific Reports 9: 17070](https://doi.org/10.1038/s41598-019-53564-w). Image on right of [deep-sea iron mats](#iron) from Hager et. al. *Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc* (2017). [Frontiers in Microbiology 8:1578](https://doi.org/10.3389/fmicb.2017.01578). * Field work photos [here](#collecting) and [here](#filtering) by [Sean Mattson](https://twitter.com/mattsonsean). * [Tree of Life](#magnitude) from Hug et. al. *A new view of the tree of life* (2016) [Nature Microbiology 1:16048](https://doi.org/10.1038/nmicrobiol.2016.48). * [DNA snippet](#genome_book) from Mori et. al. *Physiological and ecological implications of an iron- or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. nov.* (2017) [ISME Journal 11:2624-2636](https://doi.org/10.1038/ismej.2017.132). * [Microbial shapes](#10) from Park & Chess. (2012) *Foundations in Microbiology*. McGraw Hill. United States. * [Old library](#library) photo is all over the internet. I have no idea where credit should be given. * Everything else created by the author.