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Title: A communal catalogue reveals Earth’s multiscale microbial diversity

Abstract

Our growing awareness of the importance and diversity of the microbial world contrasts starkly with our limited understanding of its fundamental structure. Despite remarkable advances in DNA sequence generation, a lack of standardized protocols and common analytical framework impede useful comparison between studies, hindering development of global inferences about microbial life on Earth. Here, we show that with coordinated protocols, exact microbial 16S rRNA gene sequences can be followed across scores of individual studies, revealing patterns of diversity, community structure, and life history strategy at a planetary scale. Using 27,751 crowdsourced environmental samples comprising more than 2.2 billion reads, we find sharp divides between host-associated and free-living communities. We show that the distribution of taxonomic and sequence diversity follows consistent trends across samples types and along gradients of environmental parameters, highlighting some of the global evolutionary patterns and ecological principles that underpin Earth’s microbiome. Here, this dataset provides the most complete environmental survey of our microbial world to date, and serves as a growing reference to provide immediate global context to future microbial surveys.

Authors:
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Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1411914
Report Number(s):
PNNL-SA-123888
Journal ID: ISSN 0028-0836
Grant/Contract Number:
AC05-76RL01830
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Nature (London)
Additional Journal Information:
Journal Name: Nature (London); Journal ID: ISSN 0028-0836
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; microbiome; Earth; global

Citation Formats

Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Bárta, Jirˇí, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Mónica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frédéric, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibáñez-Álamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martín-Platero, Antonio M., Martín-Vivaldi, Manuel, Martínez, L. Margarita, Martínez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Mónica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O’Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sánchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjöling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas¸, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia. A communal catalogue reveals Earth’s multiscale microbial diversity. United States: N. p., 2017. Web. doi:10.1038/nature24621.
Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Bárta, Jirˇí, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Mónica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frédéric, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibáñez-Álamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martín-Platero, Antonio M., Martín-Vivaldi, Manuel, Martínez, L. Margarita, Martínez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Mónica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O’Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sánchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjöling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas¸, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, & Zhao, Hongxia. A communal catalogue reveals Earth’s multiscale microbial diversity. United States. doi:10.1038/nature24621.
Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob, Rivera, Jose L. Agosto, Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Bárta, Jirˇí, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric, Boyer, Donal M., Braun, Josephine, Brazelton, William, Brearley, Francis Q., Campbell, Alexandra H., Caporaso, J. Gregory, Cardona, Cesar, Carroll, JoLynn, Cary, S. Craig, Casper, Brenda B., Charles, Trevor C., Chu, Haiyan, Claar, Danielle C., Clark, Robert G., Clayton, Jonathan B., Clemente, Jose C., Cochran, Alyssa, Coleman, Maureen L., Collins, Gavin, Colwell, Rita R., Contreras, Mónica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frédéric, Dionisi, Hebe M., Dominguez-Bello, Maria Gloria, Dowell, Robin, Dubinsky, Eric A., Dunn, Peter O., Ercolini, Danilo, Espinoza, Robert E., Ezenwa, Vanessa, Fenner, Nathalie, Findlay, Helen S., Fleming, Irma D., Fogliano, Vincenzo, Forsman, Anna, Freeman, Chris, Friedman, Elliot S., Galindo, Giancarlo, Garcia, Liza, Garcia-Amado, Maria Alexandra, Garshelis, David, Gasser, Robin B., Gerdts, Gunnar, Gibson, Molly K., Gifford, Isaac, Gill, Ryan T., Giray, Tugrul, Gittel, Antje, Golyshin, Peter, Gong, Donglai, Grossart, Hans-Peter, Guyton, Kristina, Haig, Sarah-Jane, Hale, Vanessa, Hall, Ross Stephen, Hallam, Steven J., Handley, Kim M., Hasan, Nur A., Haydon, Shane R., Hickman, Jonathan E., Hidalgo, Glida, Hofmockel, Kirsten S., Hooker, Jeff, Hulth, Stefan, Hultman, Jenni, Hyde, Embriette, Ibáñez-Álamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, L. Scott, Johnston, Eric R., Joseph, Stephen, Jurburg, Stephanie D., Jurelevicius, Diogo, Karlsson, Anders, Karlsson, Roger, Kauppinen, Seth, Kellogg, Colleen T. E., Kennedy, Suzanne J., Kerkhof, Lee J., King, Gary M., Kling, George W., Koehler, Anson V., Krezalek, Monika, Kueneman, Jordan, Lamendella, Regina, Landon, Emily M., Lane-deGraaf, Kelly, LaRoche, Julie, Larsen, Peter, Laverock, Bonnie, Lax, Simon, Lentino, Miguel, Levin, Iris I., Liancourt, Pierre, Liang, Wenju, Linz, Alexandra M., Lipson, David A., Liu, Yongqin, Lladser, Manuel E., Lozada, Mariana, Spirito, Catherine M., MacCormack, Walter P., MacRae-Crerar, Aurora, Magris, Magda, Martín-Platero, Antonio M., Martín-Vivaldi, Manuel, Martínez, L. Margarita, Martínez-Bueno, Manuel, Marzinelli, Ezequiel M., Mason, Olivia U., Mayer, Gregory D., McDevitt-Irwin, Jamie M., McDonald, James E., McGuire, Krista L., McMahon, Katherine D., McMinds, Ryan, Medina, Mónica, Mendelson, Joseph R., Metcalf, Jessica L., Meyer, Folker, Michelangeli, Fabian, Miller, Kim, Mills, David A., Minich, Jeremiah, Mocali, Stefano, Moitinho-Silva, Lucas, Moore, Anni, Morgan-Kiss, Rachael M., Munroe, Paul, Myrold, David, Neufeld, Josh D., Ni, Yingying, Nicol, Graeme W., Nielsen, Shaun, Nissimov, Jozef I., Niu, Kefeng, Nolan, Matthew J., Noyce, Karen, O’Brien, Sarah L., Okamoto, Noriko, Orlando, Ludovic, Castellano, Yadira Ortiz, Osuolale, Olayinka, Oswald, Wyatt, Parnell, Jacob, Peralta-Sánchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, F. Joseph, Potter, Caitlin, Prithiviraj, Bharath, Quince, Christopher, Rani, Asha, Ranjan, Ravi, Rao, Subramanya, Rees, Andrew P., Richardson, Miles, Riebesell, Ulf, Robinson, Carol, Rockne, Karl J., Rodriguezl, Selena Marie, Rohwer, Forest, Roundstone, Wayne, Safran, Rebecca J., Sangwan, Naseer, Sanz, Virginia, Schrenk, Matthew, Schrenzel, Mark D., Scott, Nicole M., Seger, Rita L., Seguin-Orlando, Andaine, Seldin, Lucy, Seyler, Lauren M., Shakhsheer, Baddr, Sheets, Gabriela M., Shen, Congcong, Shi, Yu, Shin, Hakdong, Shogan, Benjamin D., Shutler, Dave, Siegel, Jeffrey, Simmons, Steve, Sjöling, Sara, Smith, Daniel P., Soler, Juan J., Sperling, Martin, Steinberg, Peter D., Stephens, Brent, Stevens, Melita A., Taghavi, Safiyh, Tai, Vera, Tait, Karen, Tan, Chia L., Tas¸, Neslihan, Taylor, D. Lee, Thomas, Torsten, Timling, Ina, Turner, Benjamin L., Urich, Tim, Ursell, Luke K., van der Lelie, Daniel, Van Treuren, William, van Zwieten, Lukas, Vargas-Robles, Daniela, Thurber, Rebecca Vega, Vitaglione, Paola, Walker, Donald A., Walters, William A., Wang, Shi, Wang, Tao, Weaver, Tom, Webster, Nicole S., Wehrle, Beck, Weisenhorn, Pamela, Weiss, Sophie, Werner, Jeffrey J., West, Kristin, Whitehead, Andrew, Whitehead, Susan R., Whittingham, Linda A., Willerslev, Eske, Williams, Allison E., Wood, Stephen A., Woodhams, Douglas C., Yang, Yeqin, Zaneveld, Jesse, Zarraonaindia, Iratxe, Zhang, Qikun, and Zhao, Hongxia. 2017. "A communal catalogue reveals Earth’s multiscale microbial diversity". United States. doi:10.1038/nature24621. https://www.osti.gov/servlets/purl/1411914.
@article{osti_1411914,
title = {A communal catalogue reveals Earth’s multiscale microbial diversity},
author = {Thompson, Luke R. and Sanders, Jon G. and McDonald, Daniel and Amir, Amnon and Ladau, Joshua and Locey, Kenneth J. and Prill, Robert J. and Tripathi, Anupriya and Gibbons, Sean M. and Ackermann, Gail and Navas-Molina, Jose A. and Janssen, Stefan and Kopylova, Evguenia and Vázquez-Baeza, Yoshiki and González, Antonio and Morton, James T. and Mirarab, Siavash and Zech Xu, Zhenjiang and Jiang, Lingjing and Haroon, Mohamed F. and Kanbar, Jad and Zhu, Qiyun and Jin Song, Se and Kosciolek, Tomasz and Bokulich, Nicholas A. and Lefler, Joshua and Brislawn, Colin J. and Humphrey, Gregory and Owens, Sarah M. and Hampton-Marcell, Jarrad and Berg-Lyons, Donna and McKenzie, Valerie and Fierer, Noah and Fuhrman, Jed A. and Clauset, Aaron and Stevens, Rick L. and Shade, Ashley and Pollard, Katherine S. and Goodwin, Kelly D. and Jansson, Janet K. and Gilbert, Jack A. and Knight, Rob and Rivera, Jose L. Agosto and Al-Moosawi, Lisa and Alverdy, John and Amato, Katherine R. and Andras, Jason and Angenent, Largus T. and Antonopoulos, Dionysios A. and Apprill, Amy and Armitage, David and Ballantine, Kate and Bárta, Jirˇí and Baum, Julia K. and Berry, Allison and Bhatnagar, Ashish and Bhatnagar, Monica and Biddle, Jennifer F. and Bittner, Lucie and Boldgiv, Bazartseren and Bottos, Eric and Boyer, Donal M. and Braun, Josephine and Brazelton, William and Brearley, Francis Q. and Campbell, Alexandra H. and Caporaso, J. Gregory and Cardona, Cesar and Carroll, JoLynn and Cary, S. Craig and Casper, Brenda B. and Charles, Trevor C. and Chu, Haiyan and Claar, Danielle C. and Clark, Robert G. and Clayton, Jonathan B. and Clemente, Jose C. and Cochran, Alyssa and Coleman, Maureen L. and Collins, Gavin and Colwell, Rita R. and Contreras, Mónica and Crary, Benjamin B. and Creer, Simon and Cristol, Daniel A. and Crump, Byron C. and Cui, Duoying and Daly, Sarah E. and Davalos, Liliana and Dawson, Russell D. and Defazio, Jennifer and Delsuc, Frédéric and Dionisi, Hebe M. and Dominguez-Bello, Maria Gloria and Dowell, Robin and Dubinsky, Eric A. and Dunn, Peter O. and Ercolini, Danilo and Espinoza, Robert E. and Ezenwa, Vanessa and Fenner, Nathalie and Findlay, Helen S. and Fleming, Irma D. and Fogliano, Vincenzo and Forsman, Anna and Freeman, Chris and Friedman, Elliot S. and Galindo, Giancarlo and Garcia, Liza and Garcia-Amado, Maria Alexandra and Garshelis, David and Gasser, Robin B. and Gerdts, Gunnar and Gibson, Molly K. and Gifford, Isaac and Gill, Ryan T. and Giray, Tugrul and Gittel, Antje and Golyshin, Peter and Gong, Donglai and Grossart, Hans-Peter and Guyton, Kristina and Haig, Sarah-Jane and Hale, Vanessa and Hall, Ross Stephen and Hallam, Steven J. and Handley, Kim M. and Hasan, Nur A. and Haydon, Shane R. and Hickman, Jonathan E. and Hidalgo, Glida and Hofmockel, Kirsten S. and Hooker, Jeff and Hulth, Stefan and Hultman, Jenni and Hyde, Embriette and Ibáñez-Álamo, Juan Diego and Jastrow, Julie D. and Jex, Aaron R. and Johnson, L. Scott and Johnston, Eric R. and Joseph, Stephen and Jurburg, Stephanie D. and Jurelevicius, Diogo and Karlsson, Anders and Karlsson, Roger and Kauppinen, Seth and Kellogg, Colleen T. E. and Kennedy, Suzanne J. and Kerkhof, Lee J. and King, Gary M. and Kling, George W. and Koehler, Anson V. and Krezalek, Monika and Kueneman, Jordan and Lamendella, Regina and Landon, Emily M. and Lane-deGraaf, Kelly and LaRoche, Julie and Larsen, Peter and Laverock, Bonnie and Lax, Simon and Lentino, Miguel and Levin, Iris I. and Liancourt, Pierre and Liang, Wenju and Linz, Alexandra M. and Lipson, David A. and Liu, Yongqin and Lladser, Manuel E. and Lozada, Mariana and Spirito, Catherine M. and MacCormack, Walter P. and MacRae-Crerar, Aurora and Magris, Magda and Martín-Platero, Antonio M. and Martín-Vivaldi, Manuel and Martínez, L. Margarita and Martínez-Bueno, Manuel and Marzinelli, Ezequiel M. and Mason, Olivia U. and Mayer, Gregory D. and McDevitt-Irwin, Jamie M. and McDonald, James E. and McGuire, Krista L. and McMahon, Katherine D. and McMinds, Ryan and Medina, Mónica and Mendelson, Joseph R. and Metcalf, Jessica L. and Meyer, Folker and Michelangeli, Fabian and Miller, Kim and Mills, David A. and Minich, Jeremiah and Mocali, Stefano and Moitinho-Silva, Lucas and Moore, Anni and Morgan-Kiss, Rachael M. and Munroe, Paul and Myrold, David and Neufeld, Josh D. and Ni, Yingying and Nicol, Graeme W. and Nielsen, Shaun and Nissimov, Jozef I. and Niu, Kefeng and Nolan, Matthew J. and Noyce, Karen and O’Brien, Sarah L. and Okamoto, Noriko and Orlando, Ludovic and Castellano, Yadira Ortiz and Osuolale, Olayinka and Oswald, Wyatt and Parnell, Jacob and Peralta-Sánchez, Juan M. and Petraitis, Peter and Pfister, Catherine and Pilon-Smits, Elizabeth and Piombino, Paola and Pointing, Stephen B. and Pollock, F. Joseph and Potter, Caitlin and Prithiviraj, Bharath and Quince, Christopher and Rani, Asha and Ranjan, Ravi and Rao, Subramanya and Rees, Andrew P. and Richardson, Miles and Riebesell, Ulf and Robinson, Carol and Rockne, Karl J. and Rodriguezl, Selena Marie and Rohwer, Forest and Roundstone, Wayne and Safran, Rebecca J. and Sangwan, Naseer and Sanz, Virginia and Schrenk, Matthew and Schrenzel, Mark D. and Scott, Nicole M. and Seger, Rita L. and Seguin-Orlando, Andaine and Seldin, Lucy and Seyler, Lauren M. and Shakhsheer, Baddr and Sheets, Gabriela M. and Shen, Congcong and Shi, Yu and Shin, Hakdong and Shogan, Benjamin D. and Shutler, Dave and Siegel, Jeffrey and Simmons, Steve and Sjöling, Sara and Smith, Daniel P. and Soler, Juan J. and Sperling, Martin and Steinberg, Peter D. and Stephens, Brent and Stevens, Melita A. and Taghavi, Safiyh and Tai, Vera and Tait, Karen and Tan, Chia L. and Tas¸, Neslihan and Taylor, D. Lee and Thomas, Torsten and Timling, Ina and Turner, Benjamin L. and Urich, Tim and Ursell, Luke K. and van der Lelie, Daniel and Van Treuren, William and van Zwieten, Lukas and Vargas-Robles, Daniela and Thurber, Rebecca Vega and Vitaglione, Paola and Walker, Donald A. and Walters, William A. and Wang, Shi and Wang, Tao and Weaver, Tom and Webster, Nicole S. and Wehrle, Beck and Weisenhorn, Pamela and Weiss, Sophie and Werner, Jeffrey J. and West, Kristin and Whitehead, Andrew and Whitehead, Susan R. and Whittingham, Linda A. and Willerslev, Eske and Williams, Allison E. and Wood, Stephen A. and Woodhams, Douglas C. and Yang, Yeqin and Zaneveld, Jesse and Zarraonaindia, Iratxe and Zhang, Qikun and Zhao, Hongxia},
abstractNote = {Our growing awareness of the importance and diversity of the microbial world contrasts starkly with our limited understanding of its fundamental structure. Despite remarkable advances in DNA sequence generation, a lack of standardized protocols and common analytical framework impede useful comparison between studies, hindering development of global inferences about microbial life on Earth. Here, we show that with coordinated protocols, exact microbial 16S rRNA gene sequences can be followed across scores of individual studies, revealing patterns of diversity, community structure, and life history strategy at a planetary scale. Using 27,751 crowdsourced environmental samples comprising more than 2.2 billion reads, we find sharp divides between host-associated and free-living communities. We show that the distribution of taxonomic and sequence diversity follows consistent trends across samples types and along gradients of environmental parameters, highlighting some of the global evolutionary patterns and ecological principles that underpin Earth’s microbiome. Here, this dataset provides the most complete environmental survey of our microbial world to date, and serves as a growing reference to provide immediate global context to future microbial surveys.},
doi = {10.1038/nature24621},
journal = {Nature (London)},
number = ,
volume = ,
place = {United States},
year = 2017,
month =
}

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  • Potential increases in rhizodeposition under elevated CO{sub 2} has been hypothesized to stimulate microbial activity and, therefore, alter plant nitrogen availability. We investigated nitrogen relations of a nutrient poor calcareous grassland. Plant communities with 5, 12 or 31 of the species locally present were established in field plots and exposed to ambient (356{mu}l l{sup -1}) or elevated (600{mu}l l{sup -1}) atmospheric CO{sub 2} using open-top chambers. After 5 months of CO{sub 2} exposure, soil microbial biomass, microbial activity, plant above- and belowground biomass and nitrogen contents were measured. No significant effect of elevated CO{sub 2} or plant species number onmore » soil microbial biomass or activity was observed. Elevated CO{sub 2} led to significant increases in aboveground plant biomass in the 31 spp. community only. Under elevated CO{sub 2}, net ecosystem CO{sub 2} gas exchange and fine root biomass increased in all communities. Whole plot plant nitrogen uptake did not change, but significant increases in C:N ratios of N rich forbs were found. We conclude that, although rhizodeposition appears to have increased under elevated CO{sub 2}, neither microbial biomass nor activity changed significantly. Finally, the increased amount of fine roots observed under elevated CO{sub 2} led to intensified root exploration of soil, but did not result in increased total plant nitrogen uptake.« less
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