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Front. Environ. Sci. | doi: 10.3389/fenvs.2018.00107

Spatial structuring of cellulase gene abundance and activity in soil

 Jinlyung Choi1,  Elizabeth Bach2, Jaejin Lee1, Jared Flater1, Shane Dooley1,  Adina Howe1* and  Kirsten Hofmockel3*
  • 1Agricultural and Biosystems Engineering, Iowa State University, United States
  • 2School of Global Environmental Sustainability, Colorado State University, United States
  • 3Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (DOE), United States

Microbial mechanisms controlling cellulose degradation in soil habitats remains a critical knowledge gap in understanding and modeling terrestrial carbon-cycling. We investigated land management and soil micro-habitat influences on soil bacterial communities and distribution of cellulose-degrading enzyme genes in three bioenergy cropping systems (corn, prairie, and fertilized prairie). Within the soil, aggregates have been examined as potential micro- habitats with specific characteristics influencing resource partitioning and regulation and consequently studied soil aggregate fractions from the fertilized prairie system. Soil bacterial communities and carbon-cycling gene presence varied across land management and soil microhabitats. Examination of genes specifically involved in cellulose-degradation pathways showed high levels of redundancy across the bioenergy cropping systems, but medium macroaggregates (1000-2000 um) supported greater cellulose-degrading enzyme gene abundance than other aggregate fractions and whole soil. Despite similar bacterial diversity among fertilized prairie aggregates, functional potential within the medium aggregates were predominantly associated with Actinobacteria and Proteobacteria.
These findings represent gentic potential only, and our previous work on the same samples found elevated cellulase exo-enzyme activity in microaggregates. These contrasting results emphasize the importance of measuring community, functional genes, and metabolic potentials in a coordinated manner. Together, these data indicate that location within the soil matrix matters. Overall, our results indicate that soil aggregate environments are hot-spots that select for organisms with functional attributes like cellulose degradation, and future work should further explore micro-environmental factors that affect realized C-cycling processes.

Keywords: microbiome, carbon cycling, metagenomes, aggregates, prairie, bioenergy

Received: 02 Mar 2018; Accepted: 06 Sep 2018.

Edited by:

Wilfred Otten, Abertay University, United Kingdom

Reviewed by:

Hannes Schmidt, Universität Wien, Austria
Ellard R. Hunting, Woods Hole Oceanographic Institution, United States  

Copyright: © 2018 Choi, Bach, Lee, Flater, Dooley, Howe and Hofmockel. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dr. Adina Howe, Iowa State University, Agricultural and Biosystems Engineering, Ames, 50011, Iowa, United States, adina@iastate.edu
Dr. Kirsten Hofmockel, Pacific Northwest National Laboratory (DOE), Environmental Molecular Sciences Laboratory, Richland, WA, United States, kirsten.hofmockel@pnnl.gov