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It gets the sulfide it needs to survive from a menagerie of bacteria and archaea that live in the sediments surrounding the vent. (Credit: PLoS Biology)","credit":null,"description":"tubeworms and bacteria","imgSizes":{"thumbnail":{"file":"https://ww2.kqed.org/app/uploads/sites/39/2012/05/journal.pbio640-400x225.jpg","width":400,"height":225,"mimeType":"image/jpeg"},"medium":{"file":"https://ww2.kqed.org/app/uploads/sites/39/2012/05/journal.pbio640-800x450.jpg","width":800,"height":450,"mimeType":"image/jpeg"},"post-thumbnail":{"file":"https://ww2.kqed.org/app/uploads/sites/39/2012/05/journal.pbio640-672x372.jpg","width":672,"height":372,"mimeType":"image/jpeg"},"guest-author-32":{"file":"https://ww2.kqed.org/app/uploads/sites/39/2012/05/journal.pbio640-32x32.jpg","width":32,"height":32,"mimeType":"image/jpeg"},"guest-author-64":{"file":"https://ww2.kqed.org/app/uploads/sites/39/2012/05/journal.pbio640-64x64.jpg","width":64,"height":64,"mimeType":"image/jpeg"},"guest-author-96":{"file":"https://ww2.kqed.org/app/uploads/sites/39/2012/05/journal.pbio640-96x96.jpg","width":96,"height":96,"mimeType":"image/jpeg"},"guest-author-128":{"file":"https://ww2.kqed.org/app/uploads/sites/39/2012/05/journal.pbio640-128x128.jpg","width":128,"height":128,"mimeType":"image/jpeg"},"detail":{"file":"https://ww2.kqed.org/app/uploads/sites/39/2012/05/journal.pbio640-75x75.jpg","width":75,"height":75,"mimeType":"image/jpeg"},"kqedFullSize":{"file":"https://ww2.kqed.org/app/uploads/sites/39/2012/05/journal.pbio640.jpg","width":900,"height":506}},"fetchFailed":false,"isLoading":false}},"audioPlayerReducer":{"postId":"stream_live"},"authorsReducer":{"lizagross":{"type":"authors","id":"6322","meta":{"index":"authors_1591205172","id":"6322","found":true},"name":"Liza Gross","firstName":"Liza","lastName":"Gross","slug":"lizagross","email":"lizagross@gmail.com","display_author_email":false,"staff_mastheads":[],"title":null,"bio":"Liza Gross, an award-winning independent journalist and senior editor at the biomedical journal PLOS Biology, writes mostly about conservation and public and environmental health. She was a 2013 recipient of the NYU Reporting Award, a 2013 Dennis Hunt Health Journalism fellow and a 2015 USC Data Journalism fellow.\r\n\r\nRead her \u003ca href=\"http://science.kqed.org/quest/author/lizagross/\">previous contributions\u003c/a> to \u003ca href=\"science.kqed.org/quest/\">QUEST\u003c/a>, a project dedicated to exploring the Science of Sustainability.","avatar":"https://secure.gravatar.com/avatar/1f7d36efc78088d63466cef5f10c4c7a?s=600&d=blank&r=g","twitter":null,"facebook":null,"instagram":null,"linkedin":null,"sites":[{"site":"stateofhealth","roles":["author"]},{"site":"science","roles":["author"]},{"site":"quest","roles":["subscriber"]}],"headData":{"title":"Liza Gross | KQED","description":null,"ogImgSrc":"https://secure.gravatar.com/avatar/1f7d36efc78088d63466cef5f10c4c7a?s=600&d=blank&r=g","twImgSrc":"https://secure.gravatar.com/avatar/1f7d36efc78088d63466cef5f10c4c7a?s=600&d=blank&r=g"},"isLoading":false,"link":"/author/lizagross"}},"breakingNewsReducer":{},"campaignFinanceReducer":{},"firebase":{"requesting":{},"requested":{},"timestamps":{},"data":{},"ordered":{},"auth":{"isLoaded":false,"isEmpty":true},"authError":null,"profile":{"isLoaded":false,"isEmpty":true},"listeners":{"byId":{},"allIds":[]},"isInitializing":false,"errors":[]},"navBarReducer":{"navBarId":"home","fullView":true,"showPlayer":false},"navMenuReducer":{"menus":[{"key":"menu1","items":[{"name":"News","link":"/","type":"title"},{"name":"Politics","link":"/politics"},{"name":"Science","link":"/science"},{"name":"Education","link":"/educationnews"},{"name":"Housing","link":"/housing"},{"name":"Immigration","link":"/immigration"},{"name":"Criminal Justice","link":"/criminaljustice"},{"name":"Silicon Valley","link":"/siliconvalley"},{"name":"Forum","link":"/forum"},{"name":"The California Report","link":"/californiareport"}]},{"key":"menu2","items":[{"name":"Arts & Culture","link":"/arts","type":"title"},{"name":"Critics’ Picks","link":"/thedolist"},{"name":"Cultural Commentary","link":"/artscommentary"},{"name":"Food & Drink","link":"/food"},{"name":"Bay Area Hip-Hop","link":"/bayareahiphop"},{"name":"Rebel Girls","link":"/rebelgirls"},{"name":"Arts Video","link":"/artsvideos"}]},{"key":"menu3","items":[{"name":"Podcasts","link":"/podcasts","type":"title"},{"name":"Bay Curious","link":"/podcasts/baycurious"},{"name":"Rightnowish","link":"/podcasts/rightnowish"},{"name":"The Bay","link":"/podcasts/thebay"},{"name":"On Our Watch","link":"/podcasts/onourwatch"},{"name":"Mindshift","link":"/podcasts/mindshift"},{"name":"Consider This","link":"/podcasts/considerthis"},{"name":"Political Breakdown","link":"/podcasts/politicalbreakdown"}]},{"key":"menu4","items":[{"name":"Live Radio","link":"/radio","type":"title"},{"name":"TV","link":"/tv","type":"title"},{"name":"Events","link":"/events","type":"title"},{"name":"For Educators","link":"/education","type":"title"},{"name":"Support KQED","link":"/support","type":"title"},{"name":"About","link":"/about","type":"title"},{"name":"Help Center","link":"https://kqed-helpcenter.kqed.org/s","type":"title"}]}]},"pagesReducer":{},"postsReducer":{"stream_live":{"type":"live","id":"stream_live","audioUrl":"https://streams.kqed.org/kqedradio","title":"Live Stream","excerpt":"Live Stream information currently unavailable.","link":"/radio","featImg":"","label":{"name":"KQED Live","link":"/"}},"stream_kqedNewscast":{"type":"posts","id":"stream_kqedNewscast","audioUrl":"https://www.kqed.org/.stream/anon/radio/RDnews/newscast.mp3?_=1","title":"KQED Newscast","featImg":"","label":{"name":"88.5 FM","link":"/"}},"quest_36705":{"type":"posts","id":"quest_36705","meta":{"index":"posts_1591205157","site":"quest","id":"36705","score":null,"sort":[1335970850000]},"guestAuthors":[],"slug":"classification-challenge-documenting-microbes-biodiversity%e2%80%99s-hidden-treasure","title":"Classification Challenge: Documenting Microbes, Biodiversity’s Hidden Treasure ","publishDate":1335970850,"format":"standard","headTitle":"QUEST | KQED Science","labelTerm":{"site":"quest"},"content":"\u003cfigure id=\"attachment_36715\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/05/02/classification-challenge-documenting-microbes-biodiversity%e2%80%99s-hidden-treasure/journal-pbio640/\" rel=\"attachment wp-att-36715\">\u003cimg class=\"size-thumbnail wp-image-36715\" title=\"tubeworms and bacteria\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/05/journal.pbio640-300x169.jpg\" alt=\"tubeworms and bacteria\" width=\"300\" height=\"169\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">The tubeworm Lamellibrachia luymesi lives around hydrocarbon-releasing ocean floor seeps in the Gulf ofMexico. It gets the sulfide it needs to survive from amenagerie of bacteria and archaea that live in the sedimentssurrounding the vent. (Credit: PLoS Biology)\u003c/figcaption>\u003c/figure>\n\u003cp>The impulse to classify life seems hard-wired in our species, a relic perhaps of an ancient need to forage in landscapes rife with poisonous roots, fruits, shoots and fungi. Not that the need has disappeared. You get just once chance to mistake \u003cem>Amanita phalloides\u003c/em>—aka the “death cap”—for the delectable paddy straw mushroom \u003cem>(Volvariella volvacea).\u003c/em>\u003c/p>\n\u003cp>Linnaeus’ \u003cem>Systema Naturae\u003c/em>\u003cbr>\nintroduced the modern framework for classification, helping scientists categorize life as a first step to understanding it. Taxonomists have now described roughly 1.5 million species, just a fraction of the true measure of the planet’s biodiversity.\u003c/p>\n\u003cp>Figuring out how many species inhabit Earth remains one of science’s most enduring, and elusive, challenges. A recent census effort, \u003ca href=\"http://bit.ly/IGomnF\">published last summer,\u003c/a> placed the estimate at around 8.7 million species on land and sea, with the vast majority still awaiting description.\u003c/p>\n\u003cp>The paper raised a stir, not least because its estimate of microbial diversity was so low (for bacteria, about 10,000 species), to the consternation of many, including \u003ca href=\"http://bit.ly/IGpebS\">UC Davis professor Jonathan Eisen,\u003c/a> an evolutionary biologist and microbe ambassador. But I’ll return to that in a moment.\u003c/p>\n\u003cp>Taking stock of the number of species on the planet helps biologists predict how losing them might impact ecosystems. But we’re losing species faster than biologists can discover and describe them, let alone identify the conditions they need to survive.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>As a \u003ca href=\"http://sci.odu.edu/biology/directory/Butchart%20et%20al%20Global%20biodiversity%20declines%20Science.pdf\">somber report published a few years ago\u003c/a> made clear, the Convention on Biological Diversity’s push to reduce the rate of biodiversity loss by 2010 has largely failed. Several categories of animals skirt the brink of extinction while threats to ecosystem health, from nitrogen pollution to overfishing, continue unabated.\u003c/p>\n\u003cp>Peter Kareiva, chief scientist for The Nature Conservancy, \u003ca href=\"http://breakthroughjournal.org/content/authors/peter-kareiva-robert-lalasz-an-1/conservation-in-the-anthropoce.shtml\">described our failure in an essay: \u003c/a>\u003c/p>\n\u003cp>“Biodiversity on Earth continues its rapid decline. We continue to lose forests in Africa, Asia, and Latin America. There are so few wild tigers and apes that they will be lost forever if current trends continue. Simply put, we are losing many more special places and species than we're saving.\"\u003c/p>\n\u003cp>Kareiva’s point was not that we should all hang our heads in defeat, or dig in our heels and fence off more and more land from our ever-expanding ecological footprint. He suggested something more radical: recognize the resilience of nature—not “nature” with a capital “N” but nature as a complex system of physical forces and chemical processes—and our place in it.\u003c/p>\n\u003cp>\u003cstrong>Embrace your inner microbe\u003c/strong>\u003c/p>\n\u003cp>And here’s where microbes come in.\u003c/p>\n\u003cp>Consider this: by the numbers, you’re more microbe than human. Microbes outnumber you by at least 10 to 1. Your eyelashes, hair, saliva and skin offer prime habitat to a multitude of microorganisms. What looks like a body part to you looks like a niche to microbes. When you type, you \u003ca href=\"http://www.hhmi.org/news/knight20100315.html\">leave a unique microbial fingerprint on your keyboard.\u003c/a>\u003c/p>\n\u003cp>But the real action takes place in your gut, Microbe Megalopolis, population 100 trillion, give or take a few. And here’s where it gets interesting. Your gut microflora and mine differ. And these variations can spell the difference between health and disease.\u003c/p>\n\u003cp>David Relman, a Stanford microbiologist and “microbiome” pioneer, \u003ca href=\"http://bit.ly/JACQbY\">told a reporter\u003c/a> that the diversity and individual variation of our gut microbial communities suggests that “one of the most important ecosystems on the planet might be the human body.”\u003c/p>\n\u003cfigure id=\"attachment_36708\" class=\"wp-caption alignleft\" style=\"max-width: 277px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/05/02/classification-challenge-documenting-microbes-biodiversity%e2%80%99s-hidden-treasure/cover_art1/\" rel=\"attachment wp-att-36708\">\u003cimg class=\"size-large wp-image-36708\" title=\"gut microbe\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/05/gutmicrobe-277x360.jpg\" alt=\"gut microbe\" width=\"277\" height=\"360\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">B. thetaiotaomicron, a prominent human gutbacterium, and the intestine. (Image: PLoS Biology)\u003c/figcaption>\u003c/figure>\n\u003cp>Researchers have now implicated the microbiome in allergies, autoimmune disease, obesity, and a variety of other conditions. And it all started with one study that showed that when you transplant a microbial community from one mouse to another, the phenotype--traits associated with that community, in this case, obesity--goes with it, explains Eisen. “That changed everything. Until that paper came along no one had shown that microbes played that big a role.”\u003c/p>\n\u003cp>We know microbes are the most abundant life form on Earth. But that doesn’t mean we can take them for granted. Many of their natural habitats—both landscapes and organisms—are disappearing. When host organisms disappear, the microbes will go with them. The reverse could also be true.\u003c/p>\n\u003cp>Most captive breeding programs to restore endangered species to the wild concentrate on genetic diversity as the key to survival. “But no one’s really saying we need to worry about their microbes too,” says Eisen. “No one’s focusing on whatever we need to do to make sure they have the right microbial community with them.”\u003c/p>\n\u003cp>\u003cstrong>An improbable field guide\u003c/strong>\u003c/p>\n\u003cp>About 6,000 to 8,000 species of bacteria have been described so far, but biologists like Eisen think there may be hundreds of thousands or even billions of niches to exploit. Trying to count microbe species is a losing proposition, he thinks. But trying to characterize microbe diversity by thinking in terms of niches isn’t. Microbes exploit different niches just like any other organism, from Darwin’s finches to Arctic foxes.\u003c/p>\n\u003cp>A self-described “bird nerd” since he was 7 years old, Eisen thinks the best way to get a handle on the seemingly intractable diversity of microbial life on the planet is to \u003ca href=\"http://www.youtube.com/watch?v=yoD6Fs5yRdU\">think in terms of field guides\u003c/a>. Document everything you know about different types of microbes, their niches, range, biology, genetics and ways to identify them. That becomes both a reference and an organizational framework for gathering and making sense of the mountains of data, mostly genetic, gathered from the places microbes live.\u003c/p>\n\u003cp>Using “metagenomic” tools, scientists sift through reams of genetic material extracted from environmental samples by matching gene sequences to known organisms or, if nothing matches, to something roughly similar.\u003c/p>\n\u003cp>DNA is obviously different from skeletons, bones and fossils, Eisen says, but the classification, clustering and taxonomy methods are no different from what ecologists, archeologists and paleontologists have been doing for thousands of years.\u003c/p>\n\u003cp>Even so, the microbe field guide is a tad more ambitious than any field guide to birds. The enormity of the task was perhaps best expressed by metagenomic pioneer Julian Davies in a \u003ca href=\"http://nature.berkeley.edu/brunslab/espm131/readings/gewin2006.pdf\">quote beloved by microbe hunters:\u003c/a> “Once the diversity of the microbial world is catalogued, it will make astronomy look like a pitiful science.”\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>It’s hard to overstate microbes’ importance to the planet. They drive the global carbon and nitrogen cycles that make life possible, regulate climate, purify groundwater and detoxify waste. If it weren’t for the ancient forebears of \u003ca href=\"http://bit.ly/JBGTVx\">ocean-dwelling cyanobacteria,\u003c/a> which pumped oxygen into Earth’s atmosphere after emerging some 3.5 billion years ago, we probably wouldn’t exist.\u003c/p>\n\n","blocks":[],"excerpt":"Figuring out how many species inhabit Earth remains one of science’s most enduring, and elusive, challenges.","status":"publish","parent":0,"modified":1366754060,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":26,"wordCount":1189},"headData":{"title":"Classification Challenge: Documenting Microbes, Biodiversity’s Hidden Treasure | KQED","description":"Figuring out how many species inhabit Earth remains one of science’s most enduring, and elusive, challenges.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"disqusIdentifier":"36705 http://science.kqed.org/quest/?p=36705","disqusUrl":"https://ww2.kqed.org/quest/2012/05/02/classification-challenge-documenting-microbes-biodiversity%e2%80%99s-hidden-treasure/","disqusTitle":"Classification Challenge: Documenting Microbes, Biodiversity’s Hidden Treasure ","path":"/quest/36705/classification-challenge-documenting-microbes-biodiversity%e2%80%99s-hidden-treasure","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_36715\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/05/02/classification-challenge-documenting-microbes-biodiversity%e2%80%99s-hidden-treasure/journal-pbio640/\" rel=\"attachment wp-att-36715\">\u003cimg class=\"size-thumbnail wp-image-36715\" title=\"tubeworms and bacteria\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/05/journal.pbio640-300x169.jpg\" alt=\"tubeworms and bacteria\" width=\"300\" height=\"169\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">The tubeworm Lamellibrachia luymesi lives around hydrocarbon-releasing ocean floor seeps in the Gulf ofMexico. It gets the sulfide it needs to survive from amenagerie of bacteria and archaea that live in the sedimentssurrounding the vent. (Credit: PLoS Biology)\u003c/figcaption>\u003c/figure>\n\u003cp>The impulse to classify life seems hard-wired in our species, a relic perhaps of an ancient need to forage in landscapes rife with poisonous roots, fruits, shoots and fungi. Not that the need has disappeared. You get just once chance to mistake \u003cem>Amanita phalloides\u003c/em>—aka the “death cap”—for the delectable paddy straw mushroom \u003cem>(Volvariella volvacea).\u003c/em>\u003c/p>\n\u003cp>Linnaeus’ \u003cem>Systema Naturae\u003c/em>\u003cbr>\nintroduced the modern framework for classification, helping scientists categorize life as a first step to understanding it. Taxonomists have now described roughly 1.5 million species, just a fraction of the true measure of the planet’s biodiversity.\u003c/p>\n\u003cp>Figuring out how many species inhabit Earth remains one of science’s most enduring, and elusive, challenges. A recent census effort, \u003ca href=\"http://bit.ly/IGomnF\">published last summer,\u003c/a> placed the estimate at around 8.7 million species on land and sea, with the vast majority still awaiting description.\u003c/p>\n\u003cp>The paper raised a stir, not least because its estimate of microbial diversity was so low (for bacteria, about 10,000 species), to the consternation of many, including \u003ca href=\"http://bit.ly/IGpebS\">UC Davis professor Jonathan Eisen,\u003c/a> an evolutionary biologist and microbe ambassador. But I’ll return to that in a moment.\u003c/p>\n\u003cp>Taking stock of the number of species on the planet helps biologists predict how losing them might impact ecosystems. But we’re losing species faster than biologists can discover and describe them, let alone identify the conditions they need to survive.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>As a \u003ca href=\"http://sci.odu.edu/biology/directory/Butchart%20et%20al%20Global%20biodiversity%20declines%20Science.pdf\">somber report published a few years ago\u003c/a> made clear, the Convention on Biological Diversity’s push to reduce the rate of biodiversity loss by 2010 has largely failed. Several categories of animals skirt the brink of extinction while threats to ecosystem health, from nitrogen pollution to overfishing, continue unabated.\u003c/p>\n\u003cp>Peter Kareiva, chief scientist for The Nature Conservancy, \u003ca href=\"http://breakthroughjournal.org/content/authors/peter-kareiva-robert-lalasz-an-1/conservation-in-the-anthropoce.shtml\">described our failure in an essay: \u003c/a>\u003c/p>\n\u003cp>“Biodiversity on Earth continues its rapid decline. We continue to lose forests in Africa, Asia, and Latin America. There are so few wild tigers and apes that they will be lost forever if current trends continue. Simply put, we are losing many more special places and species than we're saving.\"\u003c/p>\n\u003cp>Kareiva’s point was not that we should all hang our heads in defeat, or dig in our heels and fence off more and more land from our ever-expanding ecological footprint. He suggested something more radical: recognize the resilience of nature—not “nature” with a capital “N” but nature as a complex system of physical forces and chemical processes—and our place in it.\u003c/p>\n\u003cp>\u003cstrong>Embrace your inner microbe\u003c/strong>\u003c/p>\n\u003cp>And here’s where microbes come in.\u003c/p>\n\u003cp>Consider this: by the numbers, you’re more microbe than human. Microbes outnumber you by at least 10 to 1. Your eyelashes, hair, saliva and skin offer prime habitat to a multitude of microorganisms. What looks like a body part to you looks like a niche to microbes. When you type, you \u003ca href=\"http://www.hhmi.org/news/knight20100315.html\">leave a unique microbial fingerprint on your keyboard.\u003c/a>\u003c/p>\n\u003cp>But the real action takes place in your gut, Microbe Megalopolis, population 100 trillion, give or take a few. And here’s where it gets interesting. Your gut microflora and mine differ. And these variations can spell the difference between health and disease.\u003c/p>\n\u003cp>David Relman, a Stanford microbiologist and “microbiome” pioneer, \u003ca href=\"http://bit.ly/JACQbY\">told a reporter\u003c/a> that the diversity and individual variation of our gut microbial communities suggests that “one of the most important ecosystems on the planet might be the human body.”\u003c/p>\n\u003cfigure id=\"attachment_36708\" class=\"wp-caption alignleft\" style=\"max-width: 277px\">\u003ca href=\"http://ww2.kqed.org/quest/2012/05/02/classification-challenge-documenting-microbes-biodiversity%e2%80%99s-hidden-treasure/cover_art1/\" rel=\"attachment wp-att-36708\">\u003cimg class=\"size-large wp-image-36708\" title=\"gut microbe\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/05/gutmicrobe-277x360.jpg\" alt=\"gut microbe\" width=\"277\" height=\"360\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">B. thetaiotaomicron, a prominent human gutbacterium, and the intestine. (Image: PLoS Biology)\u003c/figcaption>\u003c/figure>\n\u003cp>Researchers have now implicated the microbiome in allergies, autoimmune disease, obesity, and a variety of other conditions. And it all started with one study that showed that when you transplant a microbial community from one mouse to another, the phenotype--traits associated with that community, in this case, obesity--goes with it, explains Eisen. “That changed everything. Until that paper came along no one had shown that microbes played that big a role.”\u003c/p>\n\u003cp>We know microbes are the most abundant life form on Earth. But that doesn’t mean we can take them for granted. Many of their natural habitats—both landscapes and organisms—are disappearing. When host organisms disappear, the microbes will go with them. The reverse could also be true.\u003c/p>\n\u003cp>Most captive breeding programs to restore endangered species to the wild concentrate on genetic diversity as the key to survival. “But no one’s really saying we need to worry about their microbes too,” says Eisen. “No one’s focusing on whatever we need to do to make sure they have the right microbial community with them.”\u003c/p>\n\u003cp>\u003cstrong>An improbable field guide\u003c/strong>\u003c/p>\n\u003cp>About 6,000 to 8,000 species of bacteria have been described so far, but biologists like Eisen think there may be hundreds of thousands or even billions of niches to exploit. Trying to count microbe species is a losing proposition, he thinks. But trying to characterize microbe diversity by thinking in terms of niches isn’t. Microbes exploit different niches just like any other organism, from Darwin’s finches to Arctic foxes.\u003c/p>\n\u003cp>A self-described “bird nerd” since he was 7 years old, Eisen thinks the best way to get a handle on the seemingly intractable diversity of microbial life on the planet is to \u003ca href=\"http://www.youtube.com/watch?v=yoD6Fs5yRdU\">think in terms of field guides\u003c/a>. Document everything you know about different types of microbes, their niches, range, biology, genetics and ways to identify them. That becomes both a reference and an organizational framework for gathering and making sense of the mountains of data, mostly genetic, gathered from the places microbes live.\u003c/p>\n\u003cp>Using “metagenomic” tools, scientists sift through reams of genetic material extracted from environmental samples by matching gene sequences to known organisms or, if nothing matches, to something roughly similar.\u003c/p>\n\u003cp>DNA is obviously different from skeletons, bones and fossils, Eisen says, but the classification, clustering and taxonomy methods are no different from what ecologists, archeologists and paleontologists have been doing for thousands of years.\u003c/p>\n\u003cp>Even so, the microbe field guide is a tad more ambitious than any field guide to birds. The enormity of the task was perhaps best expressed by metagenomic pioneer Julian Davies in a \u003ca href=\"http://nature.berkeley.edu/brunslab/espm131/readings/gewin2006.pdf\">quote beloved by microbe hunters:\u003c/a> “Once the diversity of the microbial world is catalogued, it will make astronomy look like a pitiful science.”\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"floatright"},"numeric":["floatright"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>It’s hard to overstate microbes’ importance to the planet. They drive the global carbon and nitrogen cycles that make life possible, regulate climate, purify groundwater and detoxify waste. If it weren’t for the ancient forebears of \u003ca href=\"http://bit.ly/JBGTVx\">ocean-dwelling cyanobacteria,\u003c/a> which pumped oxygen into Earth’s atmosphere after emerging some 3.5 billion years ago, we probably wouldn’t exist.\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/quest/36705/classification-challenge-documenting-microbes-biodiversity%e2%80%99s-hidden-treasure","authors":["6322"],"categories":["quest_4","quest_9"],"tags":["quest_326","quest_10936","quest_10557","quest_11055","quest_1812","quest_11054","quest_11056","quest_3307","quest_13202"],"featImg":"quest_36715","label":"quest"}},"programsReducer":{"possible":{"id":"possible","title":"Possible","info":"Possible is hosted by entrepreneur Reid Hoffman and writer Aria Finger. Together in Possible, Hoffman and Finger lead enlightening discussions about building a brighter collective future. The show features interviews with visionary guests like Trevor Noah, Sam Altman and Janette Sadik-Khan. Possible paints an optimistic portrait of the world we can create through science, policy, business, art and our shared humanity. It asks: What if everything goes right for once? How can we get there? Each episode also includes a short fiction story generated by advanced AI GPT-4, serving as a thought-provoking springboard to speculate how humanity could leverage technology for good.","airtime":"SUN 2pm","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/Possible-Podcast-Tile-360x360-1.jpg","officialWebsiteLink":"https://www.possible.fm/","meta":{"site":"news","source":"Possible"},"link":"/radio/program/possible","subscribe":{"apple":"https://podcasts.apple.com/us/podcast/possible/id1677184070","spotify":"https://open.spotify.com/show/730YpdUSNlMyPQwNnyjp4k"}},"1a":{"id":"1a","title":"1A","info":"1A is home to the national conversation. 1A brings on great guests and frames the best debate in ways that make you think, share and engage.","airtime":"MON-THU 11pm-12am","imageSrc":"https://ww2.kqed.org/radio/wp-content/uploads/sites/50/2018/04/1a.jpg","officialWebsiteLink":"https://the1a.org/","meta":{"site":"news","source":"npr"},"link":"/radio/program/1a","subscribe":{"npr":"https://rpb3r.app.goo.gl/RBrW","apple":"https://itunes.apple.com/WebObjects/MZStore.woa/wa/viewPodcast?s=143441&mt=2&id=1188724250&at=11l79Y&ct=nprdirectory","tuneIn":"https://tunein.com/radio/1A-p947376/","rss":"https://feeds.npr.org/510316/podcast.xml"}},"all-things-considered":{"id":"all-things-considered","title":"All Things Considered","info":"Every weekday, \u003cem>All Things Considered\u003c/em> hosts Robert Siegel, Audie Cornish, Ari Shapiro, and Kelly McEvers present the program's trademark mix of news, interviews, commentaries, reviews, and offbeat features. Michel Martin hosts on the weekends.","airtime":"MON-FRI 1pm-2pm, 4:30pm-6:30pm\u003cbr />SAT-SUN 5pm-6pm","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/All-Things-Considered-Podcast-Tile-360x360-1.jpg","officialWebsiteLink":"https://www.npr.org/programs/all-things-considered/","meta":{"site":"news","source":"npr"},"link":"/radio/program/all-things-considered"},"american-suburb-podcast":{"id":"american-suburb-podcast","title":"American Suburb: The Podcast","tagline":"The flip side of gentrification, told through one town","info":"Gentrification is changing cities across America, forcing people from neighborhoods they have long called home. Call them the displaced. Now those priced out of the Bay Area are looking for a better life in an unlikely place. American Suburb follows this migration to one California town along the Delta, 45 miles from San Francisco. But is this once sleepy suburb ready for them?","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/American-Suburb-Podcast-Tile-703x703-1.jpg","officialWebsiteLink":"/news/series/american-suburb-podcast","meta":{"site":"news","source":"kqed","order":"13"},"link":"/news/series/american-suburb-podcast/","subscribe":{"npr":"https://rpb3r.app.goo.gl/RBrW","apple":"https://itunes.apple.com/WebObjects/MZStore.woa/wa/viewPodcast?mt=2&id=1287748328","tuneIn":"https://tunein.com/radio/American-Suburb-p1086805/","rss":"https://ww2.kqed.org/news/series/american-suburb-podcast/feed/podcast","google":"https://podcasts.google.com/feed/aHR0cHM6Ly9mZWVkcy5tZWdhcGhvbmUuZm0vS1FJTkMzMDExODgxNjA5"}},"baycurious":{"id":"baycurious","title":"Bay Curious","tagline":"Exploring the Bay Area, one question at a time","info":"KQED’s new podcast, Bay Curious, gets to the bottom of the mysteries — both profound and peculiar — that give the Bay Area its unique identity. And we’ll do it with your help! You ask the questions. You decide what Bay Curious investigates. And you join us on the journey to find the answers.","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/Bay-Curious-Podcast-Tile-703x703-1.jpg","imageAlt":"\"KQED Bay Curious","officialWebsiteLink":"/news/series/baycurious","meta":{"site":"news","source":"kqed","order":"4"},"link":"/podcasts/baycurious","subscribe":{"apple":"https://podcasts.apple.com/us/podcast/bay-curious/id1172473406","npr":"https://www.npr.org/podcasts/500557090/bay-curious","rss":"https://ww2.kqed.org/news/category/bay-curious-podcast/feed/podcast","google":"https://podcasts.google.com/feed/aHR0cHM6Ly93dzIua3FlZC5vcmcvbmV3cy9jYXRlZ29yeS9iYXktY3VyaW91cy1wb2RjYXN0L2ZlZWQvcG9kY2FzdA","stitcher":"https://www.stitcher.com/podcast/kqed/bay-curious","spotify":"https://open.spotify.com/show/6O76IdmhixfijmhTZLIJ8k"}},"bbc-world-service":{"id":"bbc-world-service","title":"BBC World Service","info":"The day's top stories from BBC News compiled twice daily in the week, once at weekends.","airtime":"MON-FRI 9pm-10pm, TUE-FRI 1am-2am","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/BBC-World-Service-Podcast-Tile-360x360-1.jpg","officialWebsiteLink":"https://www.bbc.co.uk/sounds/play/live:bbc_world_service","meta":{"site":"news","source":"BBC World Service"},"link":"/radio/program/bbc-world-service","subscribe":{"apple":"https://itunes.apple.com/us/podcast/global-news-podcast/id135067274?mt=2","tuneIn":"https://tunein.com/radio/BBC-World-Service-p455581/","rss":"https://podcasts.files.bbci.co.uk/p02nq0gn.rss"}},"code-switch-life-kit":{"id":"code-switch-life-kit","title":"Code Switch / Life Kit","info":"\u003cem>Code Switch\u003c/em>, which listeners will hear in the first part of the hour, has fearless and much-needed conversations about race. Hosted by journalists of color, the show tackles the subject of race head-on, exploring how it impacts every part of society — from politics and pop culture to history, sports and more.\u003cbr />\u003cbr />\u003cem>Life Kit\u003c/em>, which will be in the second part of the hour, guides you through spaces and feelings no one prepares you for — from finances to mental health, from workplace microaggressions to imposter syndrome, from relationships to parenting. The show features experts with real world experience and shares their knowledge. Because everyone needs a little help being human.\u003cbr />\u003cbr />\u003ca href=\"https://www.npr.org/podcasts/510312/codeswitch\">\u003cem>Code Switch\u003c/em> offical site and podcast\u003c/a>\u003cbr />\u003ca href=\"https://www.npr.org/lifekit\">\u003cem>Life Kit\u003c/em> offical site and podcast\u003c/a>\u003cbr />","airtime":"SUN 9pm-10pm","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/Code-Switch-Life-Kit-Podcast-Tile-360x360-1.jpg","meta":{"site":"radio","source":"npr"},"link":"/radio/program/code-switch-life-kit","subscribe":{"apple":"https://podcasts.apple.com/podcast/1112190608?mt=2&at=11l79Y&ct=nprdirectory","google":"https://podcasts.google.com/feed/aHR0cHM6Ly93d3cubnByLm9yZy9yc3MvcG9kY2FzdC5waHA_aWQ9NTEwMzEy","spotify":"https://open.spotify.com/show/3bExJ9JQpkwNhoHvaIIuyV","rss":"https://feeds.npr.org/510312/podcast.xml"}},"commonwealth-club":{"id":"commonwealth-club","title":"Commonwealth Club of California Podcast","info":"The Commonwealth Club of California is the nation's oldest and largest public affairs forum. As a non-partisan forum, The Club brings to the public airwaves diverse viewpoints on important topics. The Club's weekly radio broadcast - the oldest in the U.S., dating back to 1924 - is carried across the nation on public radio stations and is now podcasting. Our website archive features audio of our recent programs, as well as selected speeches from our long and distinguished history. This podcast feed is usually updated twice a week and is always un-edited.","airtime":"THU 10pm, FRI 1am","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/Commonwealth-Club-Podcast-Tile-360x360-1.jpg","officialWebsiteLink":"https://www.commonwealthclub.org/podcasts","meta":{"site":"news","source":"Commonwealth Club of California"},"link":"/radio/program/commonwealth-club","subscribe":{"apple":"https://itunes.apple.com/us/podcast/commonwealth-club-of-california-podcast/id976334034?mt=2","google":"https://podcasts.google.com/feed/aHR0cDovL3d3dy5jb21tb253ZWFsdGhjbHViLm9yZy9hdWRpby9wb2RjYXN0L3dlZWtseS54bWw","tuneIn":"https://tunein.com/radio/Commonwealth-Club-of-California-p1060/"}},"considerthis":{"id":"considerthis","title":"Consider This","tagline":"Make sense of the day","info":"Make sense of the day. Every weekday afternoon, Consider This helps you consider the major stories of the day in less than 15 minutes, featuring the reporting and storytelling resources of NPR. Plus, KQED’s Bianca Taylor brings you the local KQED news you need to know.","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/Consider-This-Podcast-Tile-703x703-1.jpg","imageAlt":"Consider This from NPR and KQED","officialWebsiteLink":"/podcasts/considerthis","meta":{"site":"news","source":"kqed","order":"7"},"link":"/podcasts/considerthis","subscribe":{"apple":"https://podcasts.apple.com/podcast/id1503226625?mt=2&at=11l79Y&ct=nprdirectory","npr":"https://rpb3r.app.goo.gl/coronavirusdaily","google":"https://podcasts.google.com/feed/aHR0cHM6Ly9mZWVkcy5ucHIub3JnLzUxMDM1NS9wb2RjYXN0LnhtbA","spotify":"https://open.spotify.com/show/3Z6JdCS2d0eFEpXHKI6WqH"}},"forum":{"id":"forum","title":"Forum","tagline":"The conversation starts here","info":"KQED’s live call-in program discussing local, state, national and international issues, as well as in-depth interviews.","airtime":"MON-FRI 9am-11am, 10pm-11pm","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/Forum-Podcast-Tile-703x703-1.jpg","imageAlt":"KQED Forum with Mina Kim and Alexis Madrigal","officialWebsiteLink":"/forum","meta":{"site":"news","source":"kqed","order":"8"},"link":"/forum","subscribe":{"apple":"https://podcasts.apple.com/us/podcast/kqeds-forum/id73329719","google":"https://podcasts.google.com/feed/aHR0cHM6Ly9mZWVkcy5tZWdhcGhvbmUuZm0vS1FJTkM5NTU3MzgxNjMz","npr":"https://www.npr.org/podcasts/432307980/forum","stitcher":"https://www.stitcher.com/podcast/kqedfm-kqeds-forum-podcast","rss":"https://feeds.megaphone.fm/KQINC9557381633"}},"freakonomics-radio":{"id":"freakonomics-radio","title":"Freakonomics Radio","info":"Freakonomics Radio is a one-hour award-winning podcast and public-radio project hosted by Stephen Dubner, with co-author Steve Levitt as a regular guest. It is produced in partnership with WNYC.","imageSrc":"https://ww2.kqed.org/news/wp-content/uploads/sites/10/2018/05/freakonomicsRadio.png","officialWebsiteLink":"http://freakonomics.com/","airtime":"SUN 1am-2am, SAT 3pm-4pm","meta":{"site":"radio","source":"WNYC"},"link":"/radio/program/freakonomics-radio","subscribe":{"npr":"https://rpb3r.app.goo.gl/4s8b","apple":"https://itunes.apple.com/us/podcast/freakonomics-radio/id354668519","tuneIn":"https://tunein.com/podcasts/WNYC-Podcasts/Freakonomics-Radio-p272293/","rss":"https://feeds.feedburner.com/freakonomicsradio"}},"fresh-air":{"id":"fresh-air","title":"Fresh Air","info":"Hosted by Terry Gross, \u003cem>Fresh Air from WHYY\u003c/em> is the Peabody Award-winning weekday magazine of contemporary arts and issues. One of public radio's most popular programs, Fresh Air features intimate conversations with today's biggest luminaries.","airtime":"MON-FRI 7pm-8pm","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/Fresh-Air-Podcast-Tile-360x360-1.jpg","officialWebsiteLink":"https://www.npr.org/programs/fresh-air/","meta":{"site":"radio","source":"npr"},"link":"/radio/program/fresh-air","subscribe":{"npr":"https://rpb3r.app.goo.gl/4s8b","apple":"https://itunes.apple.com/WebObjects/MZStore.woa/wa/viewPodcast?s=143441&mt=2&id=214089682&at=11l79Y&ct=nprdirectory","tuneIn":"https://tunein.com/radio/Fresh-Air-p17/","rss":"https://feeds.npr.org/381444908/podcast.xml"}},"here-and-now":{"id":"here-and-now","title":"Here & Now","info":"A live production of NPR and WBUR Boston, in collaboration with stations across the country, Here & Now reflects the fluid world of news as it's happening in the middle of the day, with timely, in-depth news, interviews and conversation. Hosted by Robin Young, Jeremy Hobson and Tonya Mosley.","airtime":"MON-THU 11am-12pm","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/Here-And-Now-Podcast-Tile-360x360-1.jpg","officialWebsiteLink":"http://www.wbur.org/hereandnow","meta":{"site":"news","source":"npr"},"link":"/radio/program/here-and-now","subsdcribe":{"apple":"https://itunes.apple.com/WebObjects/MZStore.woa/wa/viewPodcast?mt=2&id=426698661","tuneIn":"https://tunein.com/radio/Here--Now-p211/","rss":"https://feeds.npr.org/510051/podcast.xml"}},"how-i-built-this":{"id":"how-i-built-this","title":"How I Built This with Guy Raz","info":"Guy Raz dives into the stories behind some of the world's best known companies. How I Built This weaves a narrative journey about innovators, entrepreneurs and idealists—and the movements they built.","imageSrc":"https://ww2.kqed.org/news/wp-content/uploads/sites/10/2018/05/howIBuiltThis.png","officialWebsiteLink":"https://www.npr.org/podcasts/510313/how-i-built-this","airtime":"SUN 7:30pm-8pm","meta":{"site":"news","source":"npr"},"link":"/radio/program/how-i-built-this","subscribe":{"npr":"https://rpb3r.app.goo.gl/3zxy","apple":"https://itunes.apple.com/us/podcast/how-i-built-this-with-guy-raz/id1150510297?mt=2","tuneIn":"https://tunein.com/podcasts/Arts--Culture-Podcasts/How-I-Built-This-p910896/","rss":"https://feeds.npr.org/510313/podcast.xml"}},"inside-europe":{"id":"inside-europe","title":"Inside Europe","info":"Inside Europe, a one-hour weekly news magazine hosted by Helen Seeney and Keith Walker, explores the topical issues shaping the continent. No other part of the globe has experienced such dynamic political and social change in recent years.","airtime":"SAT 3am-4am","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/Inside-Europe-Podcast-Tile-300x300-1.jpg","meta":{"site":"news","source":"Deutsche Welle"},"link":"/radio/program/inside-europe","subscribe":{"apple":"https://itunes.apple.com/us/podcast/inside-europe/id80106806?mt=2","tuneIn":"https://tunein.com/radio/Inside-Europe-p731/","rss":"https://partner.dw.com/xml/podcast_inside-europe"}},"latino-usa":{"id":"latino-usa","title":"Latino USA","airtime":"MON 1am-2am, SUN 6pm-7pm","info":"Latino USA, the radio journal of news and culture, is the only national, English-language radio program produced from a Latino perspective.","imageSrc":"https://ww2.kqed.org/radio/wp-content/uploads/sites/50/2018/04/latinoUsa.jpg","officialWebsiteLink":"http://latinousa.org/","meta":{"site":"news","source":"npr"},"link":"/radio/program/latino-usa","subscribe":{"npr":"https://rpb3r.app.goo.gl/xtTd","apple":"https://itunes.apple.com/WebObjects/MZStore.woa/wa/viewPodcast?s=143441&mt=2&id=79681317&at=11l79Y&ct=nprdirectory","tuneIn":"https://tunein.com/radio/Latino-USA-p621/","rss":"https://feeds.npr.org/510016/podcast.xml"}},"live-from-here-highlights":{"id":"live-from-here-highlights","title":"Live from Here Highlights","info":"Chris Thile steps to the mic as the host of Live from Here (formerly A Prairie Home Companion), a live public radio variety show. Download Chris’s Song of the Week plus other highlights from the broadcast. Produced by American Public Media.","airtime":"SAT 6pm-8pm, SUN 11am-1pm","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/Live-From-Here-Podcast-Tile-360x360-1.jpg","officialWebsiteLink":"https://www.livefromhere.org/","meta":{"site":"arts","source":"american public media"},"link":"/radio/program/live-from-here-highlights","subscribe":{"apple":"https://itunes.apple.com/us/podcast/id1167173941","tuneIn":"https://tunein.com/radio/Live-from-Here-Highlights-p921744/","rss":"https://feeds.publicradio.org/public_feeds/a-prairie-home-companion-highlights/rss/rss"}},"marketplace":{"id":"marketplace","title":"Marketplace","info":"Our flagship program, helmed by Kai Ryssdal, examines what the day in money delivered, through stories, conversations, newsworthy numbers and more. 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