Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome

McClure, Ryan; Naylor, Dan; Farris, Yuliya; Davison, Michelle; Fansler, Sarah J.; Hofmockel, Kirsten S.; Jansson, Janet K.

doi:10.3389/fmicb.2020.01987

Title: Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome

Journal Article · 25 August 2020 · Frontiers in Microbiology

DOI: https://doi.org/10.3389/fmicb.2020.01987 · OSTI ID:1650675

McClure, Ryan; Naylor, Dan; Farris, Yuliya; Davison, Michelle; Fansler, Sarah J.; Hofmockel, Kirsten S.; Jansson, Janet K.

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Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1650675

Alternate ID(s):: OSTI ID: 1673577

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 11; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: Switzerland

Language:: English

References (47)

A new medium for the enumeration and subculture of bacteria from potable water. Reasoner, D. J.; Geldreich, E. E. Applied and Environmental Microbiology, Vol. 49, Issue 1 https://doi.org/10.1128/aem.49.1.1-7.1985	journal	January 1985
Long-term pattern and magnitude of soil carbon feedback to the climate system in a warming world Melillo, J. M.; Frey, S. D.; DeAngelis, K. M. Science, Vol. 358, Issue 6359 https://doi.org/10.1126/science.aan2874	journal	October 2017
Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction: COMMUNITY DATA-DRIVEN METABOLIC NETWORK MODELING Henry, Christopher S.; Bernstein, Hans C.; Weisenhorn, Pamela Journal of Cellular Physiology, Vol. 231, Issue 11 https://doi.org/10.1002/jcp.25428	journal	June 2016
Top-Down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation Gilmore, Sean P.; Lankiewicz, Thomas S.; Wilken, St. Elmo ACS Synthetic Biology, Vol. 8, Issue 9 https://doi.org/10.1021/acssynbio.9b00271	journal	August 2019
Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior Lozano, Gabriel L.; Bravo, Juan I.; Garavito Diago, Manuel F. mBio, Vol. 10, Issue 2 https://doi.org/10.1128/mBio.02846-18	journal	March 2019
Chitin metabolism in insects: structure, function and regulation of chitin synthases and chitinases Merzendorfer, H. Journal of Experimental Biology, Vol. 206, Issue 24 https://doi.org/10.1242/jeb.00709	journal	December 2003
Soil fungal diversity in natural grasslands of the Tibetan Plateau: associations with plant diversity and productivity Yang, Teng; Adams, Jonathan M.; Shi, Yu New Phytologist, Vol. 215, Issue 2 https://doi.org/10.1111/nph.14606	journal	May 2017
Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality Jiang, Yue; Xiong, Xuejian; Danska, Jayne Microbiome, Vol. 4, Issue 1 https://doi.org/10.1186/s40168-015-0146-x	journal	January 2016
Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass Minty, Jeremy J.; Singer, Marc E.; Scholz, Scott A. Proceedings of the National Academy of Sciences, Vol. 110, Issue 36 https://doi.org/10.1073/pnas.1218447110	journal	August 2013
Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms Diamond, Spencer; Andeer, Peter F.; Li, Zhou Nature Microbiology, Vol. 4, Issue 8 https://doi.org/10.1038/s41564-019-0449-y	journal	May 2019
QIIME allows analysis of high-throughput community sequencing data Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse Nature Methods, Vol. 7, Issue 5 https://doi.org/10.1038/nmeth.f.303	journal	April 2010
EcoFABs: advancing microbiome science through standardized fabricated ecosystems Zengler, Karsten; Hofmockel, Kirsten; Baliga, Nitin S. Nature Methods, Vol. 16, Issue 7 https://doi.org/10.1038/s41592-019-0465-0	journal	June 2019
Statistical optimization for production of chitin deacetylase from Rhodococcus erythropolis HG05 Sun, Yuying; Zhang, Jiquan; Wu, Shengjun Carbohydrate Polymers, Vol. 102 https://doi.org/10.1016/j.carbpol.2013.11.010	journal	February 2014
Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States Fierer, N.; Ladau, J.; Clemente, J. C. Science, Vol. 342, Issue 6158 https://doi.org/10.1126/science.1243768	journal	October 2013
Analysis of bacterial communities in heavy metal-contaminated soils at different levels of resolution Sandaa, Ruth-Anne; Torsvik, Vigdis; Enger, ÃIvind FEMS Microbiology Ecology, Vol. 30, Issue 3 https://doi.org/10.1111/j.1574-6941.1999.tb00652.x	journal	November 1999
Chitin synthesis in human pathogenic fungi Munro, C. A.; Gow, N. A. R. Medical Mycology, Vol. 39, Issue 1 https://doi.org/10.1080/mmy.39.1.41.53	journal	January 2001
Soil Bacterial Community Shifts after Chitin Enrichment: An Integrative Metagenomic Approach Jacquiod, Samuel; Franqueville, Laure; Cécillon, Sébastien PLoS ONE, Vol. 8, Issue 11 https://doi.org/10.1371/journal.pone.0079699	journal	November 2013
Addressing the challenge of soil metaproteome complexity by improving metaproteome depth of coverage through two-dimensional liquid chromatography Callister, Stephen J.; Fillmore, Thomas L.; Nicora, Carrie D. Soil Biology and Biochemistry, Vol. 125 https://doi.org/10.1016/j.soilbio.2018.07.018	journal	October 2018
Soil bacterial networks are less stable under drought than fungal networks de Vries, Franciska T.; Griffiths, Rob I.; Bailey, Mark Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-05516-7	journal	August 2018
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks Shannon, P. Genome Research, Vol. 13, Issue 11 https://doi.org/10.1101/gr.1239303	journal	November 2003
Paving the Way From the Lab to the Field: Using Synthetic Microbial Consortia to Produce High-Quality Crops Kong, Zhaoyu; Hart, Miranda; Liu, Hongguang Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.01467	journal	October 2018
Metatranscriptomics reveals a differential temperature effect on the structural and functional organization of the anaerobic food web in rice field soil Peng, Jingjing; Wegner, Carl-Eric; Bei, Qicheng Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0546-9	journal	September 2018
Spatial and Temporal Variations in Chitinolytic Gene Expression and Bacterial Biomass Production during Chitin Degradation Baty, A. M.; Eastburn, C. C.; Techkarnjanaruk, S. Applied and Environmental Microbiology, Vol. 66, Issue 8 https://doi.org/10.1128/aem.66.8.3574-3585.2000	journal	August 2000
Selection, Succession, and Stabilization of Soil Microbial Consortia Zegeye, Elias K.; Brislawn, Colin J.; Farris, Yuliya mSystems, Vol. 4, Issue 4 https://doi.org/10.1128/mSystems.00055-19	journal	May 2019
Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations Roy Chowdhury, Taniya; Lee, Joon-Yong; Bottos, Eric M. mSystems, Vol. 4, Issue 4 https://doi.org/10.1128/mSystems.00061-19	journal	June 2019
Soil metaproteomics – Comparative evaluation of protein extraction protocols Keiblinger, Katharina M.; Wilhartitz, Inés C.; Schneider, Thomas Soil Biology and Biochemistry, Vol. 54 https://doi.org/10.1016/j.soilbio.2012.05.014	journal	November 2012
The soil microbiome — from metagenomics to metaphenomics Jansson, Janet K.; Hofmockel, Kirsten S. Current Opinion in Microbiology, Vol. 43 https://doi.org/10.1016/j.mib.2018.01.013	journal	June 2018
Environmental filtering of bacterial functional diversity along an aridity gradient Song, Ho-Kyung; Shi, Yu; Yang, Teng Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-018-37565-9	journal	January 2019
Metatranscriptomic Analysis of Arctic Peat Soil Microbiota Tveit, Alexander T.; Urich, Tim; Svenning, Mette M. Applied and Environmental Microbiology, Vol. 80, Issue 18 https://doi.org/10.1128/AEM.01030-14	journal	July 2014
Embracing the unknown: disentangling the complexities of the soil microbiome Fierer, Noah Nature Reviews Microbiology, Vol. 15, Issue 10 https://doi.org/10.1038/nrmicro.2017.87	journal	August 2017
High diversity in DNA of soil bacteria. Torsvik, V.; Goksøyr, J.; Daae, F. L. Applied and Environmental Microbiology, Vol. 56, Issue 3 https://doi.org/10.1128/aem.56.3.782-787.1990	journal	January 1990
Bottom-Up Approaches to Synthetic Cooperation in Microbial Communities Rodríguez Amor, Daniel; Dal Bello, Martina Life, Vol. 9, Issue 1 https://doi.org/10.3390/life9010022	journal	February 2019
Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome De Tender, C.; Mesuere, B.; Van der Jeugt, F. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-46106-x	journal	July 2019
Defined spatial structure stabilizes a synthetic multispecies bacterial community Kim, H. J.; Boedicker, J. Q.; Choi, J. W. Proceedings of the National Academy of Sciences, Vol. 105, Issue 47 https://doi.org/10.1073/pnas.0807935105	journal	November 2008
Landscape topography structures the soil microbiome in arctic polygonal tundra Taş, Neslihan; Prestat, Emmanuel; Wang, Shi Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-03089-z	journal	February 2018
The cell wall: a carbohydrate armour for the fungal cell Latgé, Jean-Paul Molecular Microbiology, Vol. 66, Issue 2 https://doi.org/10.1111/j.1365-2958.2007.05872.x	journal	October 2007
Programming the group behaviors of bacterial communities with synthetic cellular communication Kong, Wentao; Celik, Venhar; Liao, Chen Bioresources and Bioprocessing, Vol. 1, Issue 1 https://doi.org/10.1186/s40643-014-0024-6	journal	November 2014
Total bacterial diversity in soil and sediment communities—A review Torsvik, V.; Sørheim, R.; Goksøyr, J. Journal of Industrial Microbiology & Biotechnology, Vol. 17, Issue 3-4 https://doi.org/10.1007/bf01574690	journal	September 1996
Strategies to improve reference databases for soil microbiomes Choi, Jinlyung; Yang, Fan; Stepanauskas, Ramunas The ISME Journal, Vol. 11, Issue 4 https://doi.org/10.1038/ismej.2016.168	journal	December 2016
Characterization of Mycosphaerellaceae species associated with citrus greasy spot in Panama and Spain Aguilera-Cogley, Vidal Antonio; Berbegal, Mónica; Català, Santiago PLOS ONE, Vol. 12, Issue 12 https://doi.org/10.1371/journal.pone.0189585	journal	December 2017
Bacterial chitin degradation—mechanisms and ecophysiological strategies Beier, Sara; Bertilsson, Stefan Frontiers in Microbiology, Vol. 4 https://doi.org/10.3389/fmicb.2013.00149	journal	January 2013
Distinct Drivers of Core and Accessory Components of Soil Microbial Community Functional Diversity under Environmental Changes Zhang, Ximei; Johnston, Eric R.; Wang, Yaosheng mSystems, Vol. 4, Issue 5 https://doi.org/10.1128/mSystems.00374-19	journal	October 2019
Differentiation of Chitinase-Active and Non-Chitinase-Active Subpopulations of a Marine Bacterium during Chitin Degradation Baty, Ace M.; Eastburn, Callie C.; Diwu, Zhenjun Applied and Environmental Microbiology, Vol. 66, Issue 8 https://doi.org/10.1128/aem.66.8.3566-3573.2000	journal	August 2000
Emergent simplicity in microbial community assembly Goldford, Joshua E.; Lu, Nanxi; Bajić, Djordje Science, Vol. 361, Issue 6401 https://doi.org/10.1126/science.aat1168	journal	August 2018
Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes Hultman, Jenni; Waldrop, Mark P.; Mackelprang, Rachel Nature, Vol. 521, Issue 7551 https://doi.org/10.1038/nature14238	journal	March 2015
Wild-type Escherichia coli grows on the chitin disaccharide, N,N'-diacetylchitobiose, by expressing the cel operon Keyhani, N. O.; Roseman, S. Proceedings of the National Academy of Sciences, Vol. 94, Issue 26 https://doi.org/10.1073/pnas.94.26.14367	journal	December 1997
Rhizobium–plant signal exchange Fisher, Robert F.; Long, Sharon R. Nature, Vol. 357, Issue 6380 https://doi.org/10.1038/357655a0	journal	June 1992

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