Browsing by Author "Fierer, Noah"

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    Changes in belowground biodiversity during ecosystem development
    Delgado-Baquerizo, Manuel; Bardgett, Richard D.; Vitousek, Peter M.; Maestre, Fernando T.; Williams, Mark A.; Eldridge, David J.; Lambers, Hans; Neuhauser, Sigrid; Gallardo, Antonio; Garcia-Velazquez, Laura; Sala, Osvaldo E.; Abades, Sebastian R.; Alfaro, Fernando D.; Berhe, Asmeret Asefaw; Bowker, Matthew A.; Currier, Courtney M.; Cutler, Nick A.; Hart, Stephen C.; Hayes, Patrick E.; Hseu, Zeng-Yei; Kirchmair, Martin; Pena-Ramirez, Victor M.; Perez, Cecilia A.; Reed, Sasha C.; Santos, Fernanda; Siebe, Christina; Sullivan, Benjamin W.; Weber-Grullon, Luis; Fierer, Noah (2019-04-02)
    Belowground organisms play critical roles in maintaining multiple ecosystem processes, including plant productivity, decomposition, and nutrient cycling. Despite their importance, however, we have a limited understanding of how and why belowground biodiversity (bacteria, fungi, protists, and invertebrates) may change as soils develop over centuries to millennia (pedogenesis). Moreover, it is unclear whether belowground biodiversity changes during pedogenesis are similar to the patterns observed for aboveground plant diversity. Here we evaluated the roles of resource availability, nutrient stoichiometry, and soil abiotic factors in driving belowground biodiversity across 16 soil chronosequences (from centuries to millennia) spanning a wide range of globally distributed ecosystem types. Changes in belowground biodiversity during pedogenesis followed two main patterns. In lower-productivity ecosystems (i.e., drier and colder), increases in belowground biodiversity tracked increases in plant cover. In more productive ecosystems (i.e., wetter and warmer), increased acidification during pedogenesis was associated with declines in belowground biodiversity. Changes in the diversity of bacteria, fungi, protists, and invertebrates with pedogenesis were strongly and positively correlated worldwide, highlighting that belowground biodiversity shares similar ecological drivers as soils and ecosystems develop. In general, temporal changes in aboveground plant diversity and belowground biodiversity were not correlated, challenging the common perception that belowground biodiversity should follow similar patterns to those of plant diversity during ecosystem development. Taken together, our findings provide evidence that ecological patterns in belowground biodiversity are predictable across major globally distributed ecosystem types and suggest that shifts in plant cover and soil acidification during ecosystem development are associated with changes in belowground biodiversity over centuries to millennia.
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    A communal catalogue reveals Earth's multiscale microbial diversity
    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 (2017-11-23)
    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.
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    Environmental risk of nontuberculous mycobacterial infection: Strategies for advancing methodology
    Mercaldo, Rachel A.; Marshall, Julia E.; Cangelosi, Gerard A.; Donohue, Maura; Falkinham, Joseph O. III; Fierer, Noah; French, Joshua P.; Gebert, Matthew J.; Honda, Jennifer R.; Lipner, Ettie M.; Marras, Theodore K.; Morimoto, Kozo; Salfinger, Max; Stout, Janet; Thomson, Rachel; Prevots, Rebecca (Churchill Livingstone, 2023-03)
    The National Institute of Allergy and Infectious Diseases organized a symposium in June 2022, to facilitate discussion of the environmental risks for nontuberculous mycobacteria exposure and disease. The expert researchers presented recent studies and identified numerous research gaps. This report summarizes the discussion and identifies six major areas of future research related to culture-based and culture independent laboratory methods, alternate culture media and culturing conditions, frameworks for standardized laboratory methods, improved environmental sampling strategies, validation of exposure measures, and availability of high -quality spatiotemporal data.
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    Global ecological predictors of the soil priming effect
    Bastida, Felipe; Garcia, Carlos; Fierer, Noah; Eldridge, David J.; Bowker, Matthew A.; Abades, Sebastian R.; Alfaro, Fernando D.; Berhe, Asmeret Asefaw; Cutler, Nick A.; Gallardo, Antonio; Garcia-Velazquez, Laura; Hart, Stephen C.; Hayes, Patrick E.; Hernández, Teresa; Hseu, Zeng-Yei; Jehmlich, Nico; Kirchmair, Martin; Lambers, Hans; Neuhauser, Sigrid; Pena-Ramirez, Victor M.; Perez, Cecilia A.; Reed, Sasha C.; Santos, Fernanda; Siebe, Christina; Sullivan, Benjamin W.; Trivedi, Pankaj; Vera, Alfonso; Williams, Mark A.; Moreno, Jose Luis; Delgado-Baquerizo, Manuel (Springer Nature, 2019-08-02)
    Identifying the global drivers of soil priming is essential to understanding C cycling in terrestrial ecosystems. We conducted a survey of soils across 86 globally-distributed locations, spanning a wide range of climates, biotic communities, and soil conditions, and evaluated the apparent soil priming effect using C-13-glucose labeling. Here we show that the magnitude of the positive apparent priming effect (increase in CO2 release through accelerated microbial biomass turnover) was negatively associated with SOC content and microbial respiration rates. Our statistical modeling suggests that apparent priming effects tend to be negative in more mesic sites associated with higher SOC contents. In contrast, a single-input of labile C causes positive apparent priming effects in more arid locations with low SOC contents. Our results provide solid evidence that SOC content plays a critical role in regulating apparent priming effects, with important implications for the improvement of C cycling models under global change scenarios.
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    Identifying the diet of a declining prairie grouse using DNA metabarcoding
    Sullins, Daniel S.; Haukos, David A.; Craine, Joseph M.; Lautenbach, Joseph M.; Robinson, Samantha G.; Lautenbach, Jonathan D.; Kraft, John D.; Plumb, Reid T.; Reitz, Jonathan H.; Sandercock, Brett K.; Fierer, Noah (2018-07)
    Diets during critical brooding and winter periods likely influence the growth of Lesser Prairie-Chicken (Tympanuchus pallidicinctus) populations. During the brooding period, rapidly growing Lesser Prairie-Chicken chicks have high calorie demands and are restricted to foods within immediate surroundings. For adults and juveniles during cold winters, meeting thermoregulatory demands with available food items of limited nutrient content may be challenging. Our objective was to determine the primary animal and plant components of Lesser Prairie-Chicken diets among native prairie, cropland, and Conservation Reserve Program (CRP) fields in Kansas and Colorado, USA, during brooding and winter using a DNA metabarcoding approach. Lesser Prairie-Chicken fecal samples (n = 314) were collected during summer 2014 and winter 2014-2015, DNA was extracted, amplified, and sequenced. A region of the cytochrome oxidase I (COI) gene was sequenced to determine the arthropod component of the diet, and a portion of the trnL intron region was used to determine the plant component. Relying on fecal DNA to quantify dietary composition, as opposed to traditional visual identification of gut contents, revealed a greater proportion of soft-bodied arthropods than previously recorded. Among 80 fecal samples for which threshold arthropod DNA reads were obtained, 35% of the sequences were most likely from Lepidoptera, 26% from Orthoptera, 14% from Araneae, 13% from Hemiptera, and 12% from other orders. Plant sequences from 137 fecal samples were composed of species similar to Ambrosia (27%), followed by species similar to Lactuca or Taraxacum (10%), Medicago (6%), and Triticum (5%). Forbs were the predominant (>50% of reads) plant food consumed during both brood rearing and winter. The importance both of native forbs and of a broad array of arthropods that rely on forbs suggests that disturbance regimes that promote forbs may be crucial in providing food for Lesser Prairie-Chickens in the northern portion of their distribution.
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    The influence of soil age on ecosystem structure and function across biomes
    Delgado-Baquerizo, Manuel; Reich, Peter B.; Bardgett, Richard D.; Eldridge, David J.; Lambers, Hans; Wardle, David A.; Reed, Sasha C.; Plaza, Cesar; Png, G. Kenny; Neuhauser, Sigrid; Berhe, Asmeret Asefaw; Hart, Stephen C.; Hu, Hang-Wei; He, Ji-Zheng; Bastida, Felipe; Abades, Sebastian R.; Alfaro, Fernando D.; Cutler, Nick A.; Gallardo, Antonio; Garcia-Velazquez, Laura; Hayes, Patrick E.; Hseu, Zeng-Yei; Perez, Cecilia A.; Santos, Fernanda; Siebe, Christina; Trivedi, Pankaj; Sullivan, Benjamin W.; Weber-Grullon, Luis; Williams, Mark A.; Fierer, Noah (2020-09-18)
    The importance of soil age as an ecosystem driver across biomes remains largely unresolved. By combining a cross-biome global field survey, including data for 32 soil, plant, and microbial properties in 16 soil chronosequences, with a global meta-analysis, we show that soil age is a significant ecosystem driver, but only accounts for a relatively small proportion of the cross-biome variation in multiple ecosystem properties. Parent material, climate, vegetation and topography predict, collectively, 24 times more variation in ecosystem properties than soil age alone. Soil age is an important local-scale ecosystem driver; however, environmental context, rather than soil age, determines the rates and trajectories of ecosystem development in structure and function across biomes. Our work provides insights into the natural history of terrestrial ecosystems. We propose that, regardless of soil age, changes in the environmental context, such as those associated with global climatic and land-use changes, will have important long-term impacts on the structure and function of terrestrial ecosystems across biomes. Soil age is thought to be an important driver of ecosystem development. Here, the authors perform a global survey of soil chronosequences and meta-analysis to show that, contrary to expectations, soil age is a relatively minor ecosystem driver at the biome scale once other drivers such as parent material, climate, and vegetation type are accounted for.
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    Response of soil microbial community composition and function to a bottomland forest restoration intensity gradient
    Strickland, Michael S.; Callaham, Mac A., Jr.; Gardiner, Emile S.; Stanturf, John A.; Leff, Jonathan W.; Fierer, Noah; Bradford, Mark A. (2017-10)
    Terrestrial ecosystems are globally under threat of loss or degradation. To compensate for the impacts incurred by loss and/or degradation, efforts to restore ecosystems are being undertaken. These efforts often focus on restoring the aboveground plant community with the expectation that the belowground microbial community will follow suit. This 'Field of Dreams' expectation - if you build it, they will come - makes untested assumptions about how microbial communities and their functions will respond to aboveground-focused restoration. To determine if restoration of aboveground plant communities equates to restoration of belowground microbial communities, we assessed the effects of four forest restoration treatments - varying in intensity from unmanaged to interplanting tree species - on microbial (i.e. prokaryotic and fungal) community composition and function (i.e. catabolic profiles and extracellular enzyme activities). Additionally, effects of the restoration treatments were compared to both degraded (i.e. active arable cultivation) and target endpoint communities (i.e. remnant bottomland forest) to determine the trajectory of intensifying aboveground restoration efforts on microbial communities. Approximately 16 years after the initiation of the restoration treatments, prokaryotic and fungal community composition, and microbial function in the four restoration treatments were intermediate to the endpoint communities. Surprisingly, intensification of aboveground restoration efforts led to few differences among the four restoration treatments and increasing intensification did not consistently lead to microbial communities with greater similarity in composition and function to the target remnant forest communities. Together these results suggest that belowground microbial community composition and function will respond little to, or will lag markedly behind, intensifying aboveground restoration efforts. Reliance on a Field of Dreams' approach, even if you build it better, may still lead to belowground microbial communities that remain uncoupled from aboveground communities. Importantly, our findings suggest that restoring aboveground vegetation may not lead to the intended restoration of belowground microbial communities and the ecosystem processes they mediate.
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    The Role of Volatile Organic Compounds on Soil Microbial Communities and Ecosystem Processes
    McBride, Steven Glynn II (Virginia Tech, 2020-04-17)
    Soil microorganisms are primarily limited by carbon (C) availability. The majority of C entering belowground food webs comes directly from local flora. Plant derived labile C compounds affect microbial community structure and function, which in turn drive ecosystem function. Research has focused on dissolved organic C (DOC) from litter leachates and root exudates. These compounds are often readily assimilable by soil microorganisms and are precursors for stable soil organic matter formation. Due to diffusion limitation DOC rarely travels far beyond its origin, meaning most soil microorganisms are unable to access these compounds unless they are located near the C source. However, recent studies have illuminated the importance of volatile organic compounds (VOCs) in soil ecosystems. VOCs are produced in abundance and, as vapors, they are able to travel through soil more rapidly than DOC. This dissertation aims to investigate the importance of VOCs commonly produced during the decomposition of leaf litter. We used three separate microcosm experiments to answer the following questions. 1) How do abundant VOCs affect microbial activity in soil? 2) How do VOCs affect nitrogen (N) transformations and the microbes associated with N transformations? 3) How do VOCs affect microbial community composition? 4) Are VOCs from decomposing litter incorporated into soil C pools? In chapter 2, we show that methanol and acetone – common litter derived VOCs – increase microbial activity and labile soil C, while also decreasing available nitrate, and ammonia oxidizing archaea. Interestingly, this decrease in nitrifiers did not affect nitrification rate after VOC addition was ceased. In chapter 3, we demonstrate that soil microbial taxa respond differently to DOC and VOCs at different soil moisture levels. Specifically, DOC primarily affected taxa abundance in wetter soils, while the insoluble VOC α-pinene had the largest impact at lower moisture levels, and methanol affected abundance at all moisture levels. Finally, in chapter 4, we demonstrate that VOCs from decomposing leaf litter altered soil bacterial and fungal communities, and VOC derived C entered all measured soil organic matter pools without direct contact between decomposing litters and the soil. This work demonstrates the importance of VOCs on soil microbial communities and ecosystem function. The VOC induced increase in microbial activity, and the effects of VOCs at low moisture levels suggest that VOCs may function in the bulk soil in a manner similar to DOC in rhizosphere soil. Additionally, the incorporation of VOC-C into soil organic matter pools identifies a hitherto unrecognized mechanism for soil organic matter formation.