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4. A communal catalogue reveals Earth’s multiscale microbial diversity

Author

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, Xu, Zhenjiang Zech, 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, Agosto Rivera, Jose L., Al-Moosawi, Lisa, Alverdy, John, Amato, Katherine R., Andras, Jason, Angenent, Largus T., Antonopoulos, Dionysios A., Apprill, Amy, Armitage, David, Ballantine, Kate, Baćrta, Jirčić, 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, Gregory J., Cardona, Cesar, Carroll, JoLynn, Cary, Craig S., 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, Moćnica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frećdećric, 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, Ibaćñez-Aćlamo, Juan Diego, Jastrow, Julie D., Jex, Aaron R., Johnson, Scott L., 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, Martićn-Platero, Antonio M., Martićn-Vivaldi, Manuel, Martićnez, Margarita L., Martićnez-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, Moćnica, 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-Saćnchez, Juan M., Petraitis, Peter, Pfister, Catherine, Pilon-Smits, Elizabeth, Piombino, Paola, Pointing, Stephen B., Pollock, Joseph F., 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, Lee D., 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

Published
2017
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11. Spatial scale drives patterns in soil bacterial diversity

Author

O'Brien, Sarah L., Gibbons, Sean M., Owens, Sarah M., Hampton-Marcell, Jarrad, Johnston, Eric R., Jastrow, Julie D., Gilbert, Jack A., Meyer, Folker, and Antonopoulos, Dionysios A.

Subjects
Bacteria, Biodiversity, Panicum, Grassland, Article, Soil Microbiology
Abstract

Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure under switchgrass planted on soil historically supporting grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure between treatments within our field site or among ecosystems at a global scale. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystem scale (>10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1,772 soils from the Earth Microbiome Project, we found that 20% of bacterial taxa were shared between our site and diverse globally sourced soil samples, while grassland soils shared ∼40% of their OTUs with the current study. By spanning several orders of magnitude, our analysis suggests that extreme patchiness characterizes community structure at smaller scales but that coherent patterns emerge at longer length scales.

Published
2016

12. A communal catalogue reveals Earth's multiscale microbial diversity

Author

Biological Sciences, 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, Vazquez-Baeza, Yoshiki, Gonzalez, Antonio, Morton, James T., Mirarab, Siavash, Xu, Zhenjiang Zech, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Song, Se Jin, 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, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric M., 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, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, 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, Alexandra Garcia-Amado, Maria, 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, Ibanez-Alamo, 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 G., 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, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Margarita Martinez, L., Martinez-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, Monica, Mendelson, Joseph R., III, 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-Sanchez, 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, Sjoling, 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, Biological Sciences, 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, Vazquez-Baeza, Yoshiki, Gonzalez, Antonio, Morton, James T., Mirarab, Siavash, Xu, Zhenjiang Zech, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Song, Se Jin, 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, Barta, Jiri, Baum, Julia K., Berry, Allison, Bhatnagar, Ashish, Bhatnagar, Monica, Biddle, Jennifer F., Bittner, Lucie, Boldgiv, Bazartseren, Bottos, Eric M., 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, Monica, Crary, Benjamin B., Creer, Simon, Cristol, Daniel A., Crump, Byron C., Cui, Duoying, Daly, Sarah E., Davalos, Liliana, Dawson, Russell D., Defazio, Jennifer, Delsuc, Frederic, 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, Alexandra Garcia-Amado, Maria, 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, Ibanez-Alamo, 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 G., 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, Martin-Platero, Antonio M., Martin-Vivaldi, Manuel, Margarita Martinez, L., Martinez-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, Monica, Mendelson, Joseph R., III, 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-Sanchez, 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, Sjoling, 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

Abstract

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

Published
2017

13. Interleukin-15 promotes intestinal dysbiosis with butyrate deficiency associated with increased susceptibility to colitis

Author

Meisel, Marlies, primary, Mayassi, Toufic, additional, Fehlner-Peach, Hannah, additional, Koval, Jason C, additional, O'Brien, Sarah L, additional, Hinterleitner, Reinhard, additional, Lesko, Kathryn, additional, Kim, Sangman, additional, Bouziat, Romain, additional, Chen, Li, additional, Weber, Christopher R, additional, Mazmanian, Sarkis K, additional, Jabri, Bana, additional, and Antonopoulos, Dionysios A, additional

Published
2016
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14. Spatial scale drives patterns in soil bacterial diversity

Author

O'Brien, Sarah L., primary, Gibbons, Sean M., additional, Owens, Sarah M., additional, Hampton‐Marcell, Jarrad, additional, Johnston, Eric R., additional, Jastrow, Julie D., additional, Gilbert, Jack A., additional, Meyer, Folker, additional, and Antonopoulos, Dionysios A., additional

Published
2016
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15. Interleukin-15 promotes intestinal dysbiosis with butyrate deficiency associated with increased susceptibility to colitis.

Author

Meisel, Marlies, Mayassi, Toufic, Fehlner-Peach, Hannah, Koval, Jason C, O'Brien, Sarah L, Hinterleitner, Reinhard, Lesko, Kathryn, Kim, Sangman, Bouziat, Romain, Chen, Li, Weber, Christopher R, Mazmanian, Sarkis K, Jabri, Bana, and Antonopoulos, Dionysios A

Abstract

Dysbiosis resulting in gut-microbiome alterations with reduced butyrate production are thought to disrupt intestinal immune homeostasis and promote complex immune disorders. However, whether and how dysbiosis develops before the onset of overt pathology remains poorly defined. Interleukin-15 (IL-15) is upregulated in distressed tissue and its overexpression is thought to predispose susceptible individuals to and have a role in the pathogenesis of celiac disease and inflammatory bowel disease (IBD). Although the immunological roles of IL-15 have been largely studied, its potential impact on the microbiota remains unexplored. Analysis of 16S ribosomal RNA-based inventories of bacterial communities in mice overexpressing IL-15 in the intestinal epithelium (villin-IL-15 transgenic (v-IL-15tg) mice) shows distinct changes in the composition of the intestinal bacteria. Although some alterations are specific to individual intestinal compartments, others are found across the ileum, cecum and feces. In particular, IL-15 overexpression restructures the composition of the microbiota with a decrease in butyrate-producing bacteria that is associated with a reduction in luminal butyrate levels across all intestinal compartments. Fecal microbiota transplant experiments of wild-type and v-IL-15tg microbiota into germ-free mice further indicate that diminishing butyrate concentration observed in the intestinal lumen of v-IL-15tg mice is the result of intrinsic alterations in the microbiota induced by IL-15. This reconfiguration of the microbiota is associated with increased susceptibility to dextran sodium sulfate-induced colitis. Altogether, this study reveals that IL-15 impacts butyrate-producing bacteria and lowers butyrate levels in the absence of overt pathology, which represent events that precede and promote intestinal inflammatory diseases. [ABSTRACT FROM AUTHOR]

Published
2017
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21. Moisture and vegetation controls on decadal-scale accrual of soil organic carbon and total nitrogen in restored grasslands.

Author

O'BRIEN, SARAH L., JASTROW, JULIE D., GRIMLEY, DAVID A., and GONZALEZ-MELER, MIQUEL A.

Subjects
*SOIL restoration, *SOIL moisture, *BIODEGRADATION, *NITROGEN, *GRASSLAND restoration, *CLIMATE change, *SMOOTH brome, *TILLAGE, *VEGETATION & climate
Abstract

Revitalization of degraded landscapes may provide sinks for rising atmospheric CO2, especially in reconstructed prairies where substantial belowground productivity is coupled with large soil organic carbon (SOC) deficits after many decades of cultivation. The restoration process also provides opportunities to study the often-elusive factors that regulate soil processes. Although the precise mechanisms that govern the rate of SOC accrual are unclear, factors such as soil moisture or vegetation type may influence the net accrual rate by affecting the balance between organic matter inputs and decomposition. A resampling approach was used to assess the control that soil moisture and plant community type each exert on SOC and total nitrogen (TN) accumulation in restored grasslands. Five plots that varied in drainage were sampled at least four times over two decades to assess SOC, TN, and C4- and C3-derived C. We found that higher long-term soil moisture, characterized by low soil magnetic susceptibility, promoted SOC and TN accrual, with twice the SOC and three times the TN gain in seasonally saturated prairies compared with mesic prairies. Vegetation also influenced SOC and TN recovery, as accrual was faster in the prairies compared with C3-only grassland, and C4-derived C accrual correlated strongly to total SOC accrual but C3-C did not. High SOC accumulation at the surface (0–10 cm) combined with losses at depth (10–20 cm) suggested these soils are recovering the highly stratified profiles typical of remnant prairies. Our results suggest that local hydrology and plant community are critical drivers of SOC and TN recovery in restored grasslands. Because these factors and the way they affect SOC are susceptible to modification by climate change, we contend that predictions of the C-sequestration performance of restored grasslands must account for projected climatic changes on both soil moisture and the seasonal productivity of C4 and C3 plants. [ABSTRACT FROM AUTHOR]

Published
2010
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22. Meeting report: the 2 annual argonne soils workshop, argonne national laboratory, chicago illinois, USA, october 6-8, 2010.

Author

O'Brien SL, Glass EM, Brulc JM, Gilbert JA, Antonopoulos DA, and Meyer F

Abstract

This report summarizes the proceedings of the 2(nd) Annual Argonne Soils Workshop held at Argonne National Laboratory October 6-8, 2010. The workshop assembled a diverse group of soil ecologists, microbiologists, molecular biologists, and computational scientists to discuss the challenges and opportunities related to implementation of metagenomics approaches in soil microbial ecology. The overarching theme of the workshop was "designing ecologically meaningful soil metagenomics research", which encouraged presentations on both ecological and computational topics. The workshop fostered valuable cross-discipline communication and delivered the message that soil metagenomics research must be based on an iterative process between biological inquiry and bioinformatics tools.

Published
2011
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