The quality of organic amendments affects soil microbiome and nitrogen-cycling bacteria in an organic farming system

Ouyang, Yang; Reeve, Jennifer R.; Norton, Jeanette M.

doi:10.3389/fsoil.2022.869136

Title: The quality of organic amendments affects soil microbiome and nitrogen-cycling bacteria in an organic farming system

Journal Article · Tue Aug 02 00:00:00 EDT 2022 · Frontiers in Soil Science

DOI:https://doi.org/10.3389/fsoil.2022.869136· OSTI ID:1879554

Ouyang, Yang; Reeve, Jennifer R.; Norton, Jeanette M.

Organic amendments are applied in organic farming systems to provide nutrients for crop uptake and to improve soil health. Compost is often favored over fresh manure for food safety reasons, while fresh manure can be a valuable source of readily available nitrogen (N). However, the potential for fresh versus composted manure to differentially affect soil microbial and N-cycling functional communities over multiple seasons remains unknown. We compared the effect of composted vs. fresh cattle manure on soil microbial communities using taxonomic and functional approaches. Soils were collected from field plots with three organic N treatments: control (no amendment), composted manure (compost, 224 kg/ha total N), and fresh manure (manure, 224 kg/ha total N) in an organic production system. Illumina amplicon sequencing was used to comprehensively assess the bacterial community (16S rRNA genes), fungal community (ITS), ureolytic community ( ureC ), chitinolytic community ( chiA ), bacterial ammonia oxidizers (AOB amoA ), and nitrite oxidizers ( Nitrospira nxrB ). The results showed that both compost and manure treatment significantly changed the soil microbial communities. Manure had a stronger effect than compost on soil bacterial and fungal community composition, as well as on the ureolytic and chitinolytic communities, while compost treated soils had higher microbial richness than manure treated soils. Both taxonomic and functional approaches showed that the microbial community was more responsive to fresh manure than to compost. Manure treated soil also had more complex microbial interactions than compost treated soil. The abundance and community composition of N-cycling functional groups often played more limited roles than soil chemical properties (soil organic carbon, extractable organic carbon, and pH) in driving N-cycling processes. Results from our study may guide strategies for the management of organic amendments in organic farming systems and provide insights into the linkages between soil microbial communities and soil function.

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Sponsoring Organization:: USDOE

OSTI ID:: 1879554

Journal Information:: Frontiers in Soil Science, Journal Name: Frontiers in Soil Science Vol. 2; ISSN 2673-8619

Publisher:: Frontiers Media SACopyright Statement

Country of Publication:: Switzerland

Language:: English

References (54)

UCHIME improves sensitivity and speed of chimera detection Edgar, Robert C.; Haas, Brian J.; Clemente, Jose C. Bioinformatics, Vol. 27, Issue 16 https://doi.org/10.1093/bioinformatics/btr381	journal	June 2011
Long-term and legacy effects of manure application on soil microbial community composition Zhang, Yuting; Hao, Xiying; Alexander, Trevor W. Biology and Fertility of Soils, Vol. 54, Issue 2 https://doi.org/10.1007/s00374-017-1257-2	journal	December 2017
Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices He, Ji-zheng; Shen, Ju-pei; Zhang, Li-mei Environmental Microbiology, Vol. 9, Issue 9 https://doi.org/10.1111/j.1462-2920.2007.01358.x	journal	September 2007
Keystone taxa as drivers of microbiome structure and functioning Banerjee, Samiran; Schlaeppi, Klaus; van der Heijden, Marcel G. A. Nature Reviews Microbiology, Vol. 16, Issue 9 https://doi.org/10.1038/s41579-018-0024-1	journal	May 2018
Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships Trivedi, Pankaj; Delgado-Baquerizo, Manuel; Trivedi, Chanda The ISME Journal, Vol. 10, Issue 11 https://doi.org/10.1038/ismej.2016.65	journal	May 2016
Assessment of Biological Soil Amendments of Animal Origin Use, Research Needs, and Extension Opportunities in Organic Production Ramos, Thais Melo; Jay-Russell, Michele T.; Millner, Patricia D. Frontiers in Sustainable Food Systems, Vol. 3 https://doi.org/10.3389/fsufs.2019.00073	journal	September 2019
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy Wang, Q.; Garrity, G. M.; Tiedje, J. M. Applied and Environmental Microbiology, Vol. 73, Issue 16 https://doi.org/10.1128/AEM.00062-07	journal	June 2007
Ureolytic microbial community is modulated by fertilization regimes and particle-size fractions in a Black soil of Northeastern China Wang, Li; Luo, Xuesong; Liao, Hao Soil Biology and Biochemistry, Vol. 116 https://doi.org/10.1016/j.soilbio.2017.10.012	journal	January 2018
Bacterial diversity in soils subjected to long-term chemical fertilization can be more stably maintained with the addition of livestock manure than wheat straw Sun, Ruibo; Zhang, Xue-Xian; Guo, Xisheng Soil Biology and Biochemistry, Vol. 88 https://doi.org/10.1016/j.soilbio.2015.05.007	journal	September 2015
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
Response of soil microbial communities to compost amendments Pérez-Piqueres, Ana; Edel-Hermann, Véronique; Alabouvette, Claude Soil Biology and Biochemistry, Vol. 38, Issue 3 https://doi.org/10.1016/j.soilbio.2005.05.025	journal	March 2006
Ammonia-oxidizing bacteria are more responsive than archaea to nitrogen source in an agricultural soil Ouyang, Yang; Norton, Jeanette M.; Stark, John M. Soil Biology and Biochemistry, Vol. 96 https://doi.org/10.1016/j.soilbio.2016.01.012	journal	May 2016
Shifts in Nitrobacter- and Nitrospira-like nitrite-oxidizing bacterial communities under long-term fertilization practices Han, Shun; Zeng, Luyang; Luo, Xuesong Soil Biology and Biochemistry, Vol. 124 https://doi.org/10.1016/j.soilbio.2018.05.033	journal	September 2018
Impacts of inorganic and organic fertilization treatments on bacterial and fungal communities in a paddy soil Wang, Jichen; Song, Yang; Ma, Tengfei Applied Soil Ecology, Vol. 112 https://doi.org/10.1016/j.apsoil.2017.01.005	journal	April 2017
Ribosomal Database Project: data and tools for high throughput rRNA analysis Cole, James R.; Wang, Qiong; Fish, Jordan A. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1244	journal	November 2013
Short-Term Nitrogen Fertilization Affects Microbial Community Composition and Nitrogen Mineralization Functions in an Agricultural Soil Ouyang, Yang; Norton, Jeanette M. Applied and Environmental Microbiology, Vol. 86, Issue 5 https://doi.org/10.1128/AEM.02278-19	journal	December 2019
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data McMurdie, Paul J.; Holmes, Susan PLoS ONE, Vol. 8, Issue 4 https://doi.org/10.1371/journal.pone.0061217	journal	April 2013
Controls and Adaptive Management of Nitrification in Agricultural Soils Norton, Jeanette; Ouyang, Yang Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01931	journal	August 2019
Bacterial Chitinolytic Communities Respond to Chitin and pH Alteration in Soil Kielak, Anna M.; Cretoiu, Mariana Silvia; Semenov, Alexander V. Applied and Environmental Microbiology, Vol. 79, Issue 1 https://doi.org/10.1128/AEM.02546-12	journal	January 2013
UPARSE: highly accurate OTU sequences from microbial amplicon reads Edgar, Robert C. Nature Methods, Vol. 10, Issue 10 https://doi.org/10.1038/nmeth.2604	journal	August 2013
Chitin degradation and the temporary response of bacterial chitinolytic communities to chitin amendment in soil under different fertilization regimes Hui, Cai; Jiang, Hui; Liu, Bing Science of The Total Environment, Vol. 705 https://doi.org/10.1016/j.scitotenv.2019.136003	journal	February 2020
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
Molecular ecological network analyses Deng, Ye; Jiang, Yi-Huei; Yang, Yunfeng BMC Bioinformatics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2105-13-113	journal	January 2012
Long-term successional dynamics of microbial association networks in anaerobic digestion processes Wu, Linwei; Yang, Yunfeng; Chen, Si Water Research, Vol. 104 https://doi.org/10.1016/j.watres.2016.07.072	journal	November 2016
Effects of cover crops, compost, and manure amendments on soil microbial community structure in tomato production systems Carrera, L. M.; Buyer, J. S.; Vinyard, B. Applied Soil Ecology, Vol. 37, Issue 3 https://doi.org/10.1016/J.APSOIL.2007.08.003	journal	November 2007
Soil enzyme activities and abundance of microbial functional genes involved in nitrogen transformations in an organic farming system Ouyang, Yang; Reeve, Jennifer R.; Norton, Jeanette M. Biology and Fertility of Soils, Vol. 54, Issue 4 https://doi.org/10.1007/s00374-018-1272-y	journal	March 2018
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
Influence of Manure Application on the Soil Bacterial Microbiome in Integrated Crop-Livestock Farms in Maryland Peng, Mengfei; Tabashsum, Zajeba; Millner, Patricia Microorganisms, Vol. 9, Issue 12 https://doi.org/10.3390/microorganisms9122586	journal	December 2021
Organic farming enhances soil microbial abundance and activity—A meta-analysis and meta-regression Lori, Martina; Symnaczik, Sarah; Mäder, Paul PLOS ONE, Vol. 12, Issue 7 https://doi.org/10.1371/journal.pone.0180442	journal	July 2017
FunGene: the functional gene pipeline and repository Fish, Jordan A.; Chai, Benli; Wang, Qiong Frontiers in Microbiology, Vol. 4 https://doi.org/10.3389/fmicb.2013.00291	journal	January 2013
A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria Daims, Holger; Lücker, Sebastian; Wagner, Michael Trends in Microbiology, Vol. 24, Issue 9 https://doi.org/10.1016/j.tim.2016.05.004	journal	September 2016
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples: Primers for marine microbiome studies Parada, Alma E.; Needham, David M.; Fuhrman, Jed A. Environmental Microbiology, Vol. 18, Issue 5 https://doi.org/10.1111/1462-2920.13023	journal	October 2015
Ecological Patterns of nifH Genes in Four Terrestrial Climatic Zones Explored with Targeted Metagenomics Using FrameBot, a New Informatics Tool Wang, Qiong; Quensen, John F.; Fish, Jordan A. mBio, Vol. 4, Issue 5 https://doi.org/10.1128/mBio.00592-13	journal	September 2013
Gephi: An Open Source Software for Exploring and Manipulating Networks Bastian, Mathieu; Heymann, Sebastien; Jacomy, Mathieu Proceedings of the International AAAI Conference on Web and Social Media, Vol. 3, Issue 1 https://doi.org/10.1609/icwsm.v3i1.13937	journal	March 2009
Bacterial communities in chitin-amended soil as revealed by 16S rRNA gene based pyrosequencing Cretoiu, Mariana Silvia; Kielak, Anna Maria; Schluter, Andreas Soil Biology and Biochemistry, Vol. 76 https://doi.org/10.1016/j.soilbio.2014.04.027	journal	September 2014
Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots Banerjee, Samiran; Walder, Florian; Büchi, Lucie The ISME Journal, Vol. 13, Issue 7 https://doi.org/10.1038/s41396-019-0383-2	journal	March 2019
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
A meta-analysis of changes in bacterial and archaeal communities with time Shade, Ashley; Gregory Caporaso, J.; Handelsman, Jo The ISME Journal, Vol. 7, Issue 8 https://doi.org/10.1038/ismej.2013.54	journal	April 2013
Nitrite Oxidizer Activity and Community Are More Responsive Than Their Abundance to Ammonium-Based Fertilizer in an Agricultural Soil Ouyang, Yang; Norton, Jeanette M. Frontiers in Microbiology, Vol. 11 https://doi.org/10.3389/fmicb.2020.01736	journal	August 2020
First exploration of Nitrobacter diversity in soils by a PCR cloning-sequencing approach targeting functional gene nxrA: nxrA diversity in soils Poly, Franck; Wertz, Sophie; Brothier, Elisabeth FEMS Microbiology Ecology, Vol. 63, Issue 1 https://doi.org/10.1111/j.1574-6941.2007.00404.x	journal	January 2008
Nitrogen Mineralization: Challenges of a Changing Paradigm Schimel, Joshua P.; Bennett, Jennifer Ecology, Vol. 85, Issue 3 https://doi.org/10.1890/03-8002	journal	March 2004
Insight into how organic amendments can shape the soil microbiome in long-term field experiments as revealed by network analysis Ling, Ning; Zhu, Chen; Xue, Chao Soil Biology and Biochemistry, Vol. 99 https://doi.org/10.1016/j.soilbio.2016.05.005	journal	August 2016
Structure and function of the soil microbial community in a long-term fertilizer experiment Marschner, P. Soil Biology and Biochemistry, Vol. 35, Issue 3 https://doi.org/10.1016/S0038-0717(02)00297-3	journal	March 2003
Distinct soil microbial diversity under long-term organic and conventional farming Hartmann, Martin; Frey, Beat; Mayer, Jochen The ISME Journal, Vol. 9, Issue 5 https://doi.org/10.1038/ismej.2014.210	journal	October 2014
Molecular biology of microbial ureases Mobley, H. L.; Island, M. D.; Hausinger, R. P. Microbiological Reviews, Vol. 59, Issue 3 https://doi.org/10.1128/mr.59.3.451-480.1995	journal	September 1995
Compost, rapeseed rotation, and biocontrol agents significantly impact soil microbial communities in organic and conventional potato production systems Bernard, Edward; Larkin, Robert P.; Tavantzis, Stellos Applied Soil Ecology, Vol. 52 https://doi.org/10.1016/j.apsoil.2011.10.002	journal	January 2012
Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming Hartman, Kyle; van der Heijden, Marcel G. A.; Wittwer, Raphaël A. Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-017-0389-9	journal	January 2018
NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing N itrospira : Functional and phylogenetic marker for Pester, Michael; Maixner, Frank; Berry, David Environmental Microbiology, Vol. 16, Issue 10 https://doi.org/10.1111/1462-2920.12300	journal	November 2013
Organic Amendments in a Long-term Field Trial—Consequences for the Bulk Soil Bacterial Community as Revealed by Network Analysis Schmid, Christoph A. O.; Schröder, Peter; Armbruster, Martin Microbial Ecology, Vol. 76, Issue 1 https://doi.org/10.1007/s00248-017-1110-z	journal	November 2017
The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages Shi, Shengjing; Nuccio, Erin E.; Shi, Zhou J. Ecology Letters, Vol. 19, Issue 8 https://doi.org/10.1111/ele.12630	journal	June 2016
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Love, Michael I.; Huber, Wolfgang; Anders, Simon Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0550-8	journal	December 2014
Organic amendments increase crop yields by improving microbe-mediated soil functioning of agroecosystems: A meta-analysis Luo, Gongwen; Li, Ling; Friman, Ville-Petri Soil Biology and Biochemistry, Vol. 124 https://doi.org/10.1016/j.soilbio.2018.06.002	journal	September 2018
The Ecology and Evolution of Microbial Competition Ghoul, Melanie; Mitri, Sara Trends in Microbiology, Vol. 24, Issue 10 https://doi.org/10.1016/j.tim.2016.06.011	journal	October 2016
Functional Molecular Ecological Networks Zhou, Jizhong; Deng, Ye; Luo, Feng mBio, Vol. 1, Issue 4 https://doi.org/10.1128/mBio.00169-10	journal	October 2010

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