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Title: Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States

The North American prairie covered about 3.6 million-km 2 of the continent prior to European contact. Only 1–2% of the original prairie remains, but the soils that developed under these prairies are some of the most productive and fertile in the world, containing over 35% of the soil carbon in the continental United States. Cultivation may alter microbial diversity and composition, influencing the metabolism of carbon, nitrogen, and other elements. Here, we explored the structure and functional potential of the soil microbiome in paired cultivated-corn (at the time of sampling) and never-cultivated native prairie soils across a three-states transect (Wisconsin, Iowa, and Kansas) using metagenomic and 16S rRNA gene sequencing and lipid analysis. At the Wisconsin site, we also sampled adjacent restored prairie and switchgrass plots. We found that agricultural practices drove differences in community composition and diversity across the transect. Microbial biomass in prairie samples was twice that of cultivated soils, but alpha diversity was higher with cultivation. Metagenome analyses revealed denitrification and starch degradation genes were abundant across all soils, as were core genes involved in response to osmotic stress, resource transport, and environmental sensing. Together, these data indicate that cultivation shifted the microbiome in consistent ways acrossmore » different regions of the prairie, but also suggest that many functions are resilient to changes caused by land management practices – perhaps reflecting adaptations to conditions common to tallgrass prairie soils in the region (e.g., soil type, parent material, development under grasses, temperature and rainfall patterns, and annual freeze-thaw cycles). These findings are important for understanding the long-term consequences of land management practices to prairie soil microbial communities and their genetic potential to carry out key functions.« less
Authors:
 [1] ;  [2] ;  [2] ;  [3] ;  [4] ;  [5] ;  [6] ;  [7] ;  [1] ;  [1] ;  [4] ;  [3] ;  [8]
  1. California State Univ., Northridge, CA (United States). Dept. of Biology
  2. Juniata College, Huntingdon, PA (United States). Dept. of Biology
  3. Michigan State Univ., East Lansing, MI (United States). Center for Microbial Ecology; Univ. of Wisconsin, Madison, WI (United States). Great Lakes Bioenergy Research Center
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  5. Univ. of Wisconsin, Madison, WI (United States). Great Lakes Bioenergy Research Center; Chinese Academy of Sciences (CAS), Beijing (China). Inst. of Applied Ecology
  6. Univ. of Wisconsin, Madison, WI (United States). Great Lakes Bioenergy Research Center. Dept. of Agronomy
  7. Kansas State Univ., Manhattan, KS (United States). Dept. of Agronomy
  8. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Earth and Biological Sciences Directorate
Publication Date:
Grant/Contract Number:
AC02-05CH11231; AC05-76RL01830; FC02-07ER64494; DBI-1248096; RCN 1051481
Type:
Published Article
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 9; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Research Org:
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of Wisconsin, Madison, WI (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Juniata College, Huntingdon, PA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); PNNL Laboratory Directed Research and Development (LDRD) Program; National Science Foundation (NSF); Howard Hughes Medical Inst. (HHMI) (United States)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; soil microbiome; land management; metagenomics; native prairie; climate change; carbon cycle; nitrogen cycle
OSTI Identifier:
1464646
Alternate Identifier(s):
OSTI ID: 1477362

Mackelprang, Rachel, Grube, Alyssa M., Lamendella, Regina, Jesus, Ederson da C., Copeland, Alex, Liang, Chao, Jackson, Randall D., Rice, Charles W., Kapucija, Stefanie, Parsa, Bayan, Tringe, Susannah G., Tiedje, James M., and Jansson, Janet K.. Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States. United States: N. p., Web. doi:10.3389/fmicb.2018.01775.
Mackelprang, Rachel, Grube, Alyssa M., Lamendella, Regina, Jesus, Ederson da C., Copeland, Alex, Liang, Chao, Jackson, Randall D., Rice, Charles W., Kapucija, Stefanie, Parsa, Bayan, Tringe, Susannah G., Tiedje, James M., & Jansson, Janet K.. Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States. United States. doi:10.3389/fmicb.2018.01775.
Mackelprang, Rachel, Grube, Alyssa M., Lamendella, Regina, Jesus, Ederson da C., Copeland, Alex, Liang, Chao, Jackson, Randall D., Rice, Charles W., Kapucija, Stefanie, Parsa, Bayan, Tringe, Susannah G., Tiedje, James M., and Jansson, Janet K.. 2018. "Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States". United States. doi:10.3389/fmicb.2018.01775.
@article{osti_1464646,
title = {Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States},
author = {Mackelprang, Rachel and Grube, Alyssa M. and Lamendella, Regina and Jesus, Ederson da C. and Copeland, Alex and Liang, Chao and Jackson, Randall D. and Rice, Charles W. and Kapucija, Stefanie and Parsa, Bayan and Tringe, Susannah G. and Tiedje, James M. and Jansson, Janet K.},
abstractNote = {The North American prairie covered about 3.6 million-km2 of the continent prior to European contact. Only 1–2% of the original prairie remains, but the soils that developed under these prairies are some of the most productive and fertile in the world, containing over 35% of the soil carbon in the continental United States. Cultivation may alter microbial diversity and composition, influencing the metabolism of carbon, nitrogen, and other elements. Here, we explored the structure and functional potential of the soil microbiome in paired cultivated-corn (at the time of sampling) and never-cultivated native prairie soils across a three-states transect (Wisconsin, Iowa, and Kansas) using metagenomic and 16S rRNA gene sequencing and lipid analysis. At the Wisconsin site, we also sampled adjacent restored prairie and switchgrass plots. We found that agricultural practices drove differences in community composition and diversity across the transect. Microbial biomass in prairie samples was twice that of cultivated soils, but alpha diversity was higher with cultivation. Metagenome analyses revealed denitrification and starch degradation genes were abundant across all soils, as were core genes involved in response to osmotic stress, resource transport, and environmental sensing. Together, these data indicate that cultivation shifted the microbiome in consistent ways across different regions of the prairie, but also suggest that many functions are resilient to changes caused by land management practices – perhaps reflecting adaptations to conditions common to tallgrass prairie soils in the region (e.g., soil type, parent material, development under grasses, temperature and rainfall patterns, and annual freeze-thaw cycles). These findings are important for understanding the long-term consequences of land management practices to prairie soil microbial communities and their genetic potential to carry out key functions.},
doi = {10.3389/fmicb.2018.01775},
journal = {Frontiers in Microbiology},
number = ,
volume = 9,
place = {United States},
year = {2018},
month = {8}
}

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