Spatial Structuring of Cellulase Gene Abundance and Activity in Soil
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 e...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-10-01
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| Series: | Frontiers in Environmental Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fenvs.2018.00107/full |
| _version_ | 1819123671136993280 |
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| author | Jinlyung Choi Elizabeth Bach Elizabeth Bach Jaejin Lee Jared Flater Shane Dooley Adina Howe Kirsten S. Hofmockel Kirsten S. Hofmockel |
| author_facet | Jinlyung Choi Elizabeth Bach Elizabeth Bach Jaejin Lee Jared Flater Shane Dooley Adina Howe Kirsten S. Hofmockel Kirsten S. Hofmockel |
| author_sort | Jinlyung Choi |
| collection | DOAJ |
| description | 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, thus we also investigated genes associated with cellulose degradation within 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 (1,000–2,000 μm) supported greater cellulose-degrading enzyme gene abundance than other aggregate fractions and whole soil. In medium aggregates, the enriched cellulose-degrading genes were most similar to genes previously observed in Actinobacteria. 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. |
| first_indexed | 2024-12-22T07:12:03Z |
| format | Article |
| id | doaj.art-9d5600b4876443739eca62650a139982 |
| institution | Directory Open Access Journal |
| issn | 2296-665X |
| language | English |
| last_indexed | 2024-12-22T07:12:03Z |
| publishDate | 2018-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Environmental Science |
| spelling | doaj.art-9d5600b4876443739eca62650a1399822022-12-21T18:34:29ZengFrontiers Media S.A.Frontiers in Environmental Science2296-665X2018-10-01610.3389/fenvs.2018.00107368512Spatial Structuring of Cellulase Gene Abundance and Activity in SoilJinlyung Choi0Elizabeth Bach1Elizabeth Bach2Jaejin Lee3Jared Flater4Shane Dooley5Adina Howe6Kirsten S. Hofmockel7Kirsten S. Hofmockel8Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United StatesDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United StatesDepartment of Biology and School of Global Environmental Sustainability, Colorado State University, Fort Collins, CO, United StatesDepartment of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United StatesDepartment of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United StatesDepartment of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United StatesDepartment of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United StatesDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United StatesEnvironmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United StatesMicrobial 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, thus we also investigated genes associated with cellulose degradation within 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 (1,000–2,000 μm) supported greater cellulose-degrading enzyme gene abundance than other aggregate fractions and whole soil. In medium aggregates, the enriched cellulose-degrading genes were most similar to genes previously observed in Actinobacteria. 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.https://www.frontiersin.org/article/10.3389/fenvs.2018.00107/fullmicrobiomecarbon cyclingmetagenomesaggregatesprairiebioenergy |
| spellingShingle | Jinlyung Choi Elizabeth Bach Elizabeth Bach Jaejin Lee Jared Flater Shane Dooley Adina Howe Kirsten S. Hofmockel Kirsten S. Hofmockel Spatial Structuring of Cellulase Gene Abundance and Activity in Soil Frontiers in Environmental Science microbiome carbon cycling metagenomes aggregates prairie bioenergy |
| title | Spatial Structuring of Cellulase Gene Abundance and Activity in Soil |
| title_full | Spatial Structuring of Cellulase Gene Abundance and Activity in Soil |
| title_fullStr | Spatial Structuring of Cellulase Gene Abundance and Activity in Soil |
| title_full_unstemmed | Spatial Structuring of Cellulase Gene Abundance and Activity in Soil |
| title_short | Spatial Structuring of Cellulase Gene Abundance and Activity in Soil |
| title_sort | spatial structuring of cellulase gene abundance and activity in soil |
| topic | microbiome carbon cycling metagenomes aggregates prairie bioenergy |
| url | https://www.frontiersin.org/article/10.3389/fenvs.2018.00107/full |
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