Agricultural practices influence soil microbiome assembly and interactions at different depths identified by machine learning

Mo, Yujie; Bier, Raven; Li, Xiaolin; Daniels, Melinda; Smith, Andrew; Yu, Lei; Kan, Jinjun

doi:10.1038/s42003-024-07059-8

Title: Agricultural practices influence soil microbiome assembly and interactions at different depths identified by machine learning

Journal Article · 18 October 2024 · Communications Biology

DOI: https://doi.org/10.1038/s42003-024-07059-8 · OSTI ID:2477930

^[1];

^[2]; Li, Xiaolin ^[3]; Daniels, Melinda ^[4];

^[5];

^[1];

^[4]

Beihang University, Beijing (China)
Stroud Water Research Center, Avondale, PA (United States); University of Georgia, Aiken, SC (United States)
Zibo Vocational Institute, Shandong (China)
Stroud Water Research Center, Avondale, PA (United States)
Rodale Institute, Kutztown, PA (United States)

Agricultural practices affect soil microbes which are critical to soil health and sustainable agriculture. To understand prokaryotic and fungal assembly under agricultural practices, we use machine learning-based methods. We show that fertility source is the most pronounced factor for microbial assembly especially for fungi, and its effect decreases with soil depths. Fertility source also shapes microbial co-occurrence patterns revealed by machine learning, leading to fungi-dominated modules sensitive to fertility down to 30 cm depth. Tillage affects soil microbiomes at 0-20 cm depth, enhancing dispersal and stochastic processes but potentially jeopardizing microbial interactions. Cover crop effects are less pronounced and lack depth-dependent patterns. Machine learning reveals that the impact of agricultural practices on microbial communities is multifaceted and highlights the role of fertility source over the soil depth. Machine learning overcomes the linear limitations of traditional methods and offers enhanced insights into the mechanisms underlying microbial assembly and distributions in agriculture soils.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Savannah River Ecology Laboratory (SREL), Aiken, SC (United States)

Sponsoring Organization:: USDOE Office of Environmental Management (EM)

Grant/Contract Number:: EM0005228

OSTI ID:: 2477930

Journal Information:: Communications Biology, Journal Name: Communications Biology Journal Issue: 1 Vol. 7; ISSN 2399-3642

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

References (106)

Comparison of distance‐based and model‐based ordinations Roberts, David W. Ecology, Vol. 101, Issue 1 https://doi.org/10.1002/ecy.2908	journal	November 2019
Predicting microbiome compositions from species assemblages through deep learning Michel‐Mata, Sebastian; Wang, Xu‐Wen; Liu, Yang‐Yu iMeta, Vol. 1, Issue 1 https://doi.org/10.1002/imt2.3	journal	March 2022
Assessing the impact of organic versus conventional agricultural management on soil hydraulic properties in a long‐term experiment Alfahham, Abdelrahman; Amato, Matthew T.; Omondi, Emmanuel Soil Science Society of America Journal, Vol. 85, Issue 6 https://doi.org/10.1002/saj2.20314	journal	September 2021
Multidimensional scaling: I. Theory and method Torgerson, Warren S. Psychometrika, Vol. 17, Issue 4 https://doi.org/10.1007/BF02288916	journal	December 1952
Crop microbiome: their role and advances in molecular and omic techniques for the sustenance of agriculture Rai, Shalini; Omar, Ayman F.; Rehan, Medhat Planta, Vol. 257, Issue 2 https://doi.org/10.1007/s00425-022-04052-5	journal	December 2022
Quantifying structural redundancy in ecological communities Clarke, K. R.; Warwick, R. M. Oecologia, Vol. 113, Issue 2 https://doi.org/10.1007/s004420050379	journal	January 1998
Deep soil organic matter—a key but poorly understood component of terrestrial C cycle Rumpel, Cornelia; Kögel-Knabner, Ingrid Plant and Soil, Vol. 338, Issue 1-2 https://doi.org/10.1007/s11104-010-0391-5	journal	May 2010
Stochastic processes dominate assembly of soil fungal community in grazing excluded grasslands in northwestern China Guo, Qian; Wen, Zhongming; Ghanizadeh, Hossein Journal of Soils and Sediments, Vol. 23, Issue 1 https://doi.org/10.1007/s11368-022-03315-8	journal	August 2022
Dictyosporiaceae fam. nov. Boonmee, Saranyaphat; D’souza, Melvina J.; Luo, Zonglong Fungal Diversity, Vol. 80, Issue 1 https://doi.org/10.1007/s13225-016-0363-z	journal	April 2016
Effects of tillage on runoff and erosion patterns Takken, Ingrid; Govers, Gerard; Jetten, Victor Soil and Tillage Research, Vol. 61, Issue 1-2 https://doi.org/10.1016/S0167-1987(01)00178-7	journal	August 2001
Agricultural soil microbiomes differentiate in soil profiles with fertility source, tillage, and cover crops Bier, Raven L.; Daniels, Melinda; Oviedo-Vargas, Diana Agriculture, Ecosystems & Environment, Vol. 368 https://doi.org/10.1016/j.agee.2024.109002	journal	July 2024
Explaining individual predictions when features are dependent: More accurate approximations to Shapley values Aas, Kjersti; Jullum, Martin; Løland, Anders Artificial Intelligence, Vol. 298 https://doi.org/10.1016/j.artint.2021.103502	journal	September 2021
Plant microbiome structure and benefits for sustainable agriculture Santos, Lidiane Figueiredo; Olivares, Fabio Lopes Current Plant Biology, Vol. 26 https://doi.org/10.1016/j.cpb.2021.100198	journal	June 2021
A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application Compant, Stéphane; Samad, Abdul; Faist, Hanna Journal of Advanced Research, Vol. 19 https://doi.org/10.1016/j.jare.2019.03.004	journal	September 2019
Enhance explainability of manifold learning Han, Henry; Li, Wentian; Wang, Jiacun Neurocomputing, Vol. 500 https://doi.org/10.1016/j.neucom.2022.05.119	journal	August 2022
Application of random matrix theory to biological networks Luo, Feng; Zhong, Jianxin; Yang, Yunfeng Physics Letters A, Vol. 357, Issue 6 https://doi.org/10.1016/j.physleta.2006.04.076	journal	September 2006
Effects of tillage practices on soil microbiome and agricultural parameters Kraut-Cohen, Judith; Zolti, Avihai; Shaltiel-Harpaz, Liora Science of The Total Environment, Vol. 705 https://doi.org/10.1016/j.scitotenv.2019.135791	journal	February 2020
Stochastic processes drive bacterial and fungal community assembly in sustainable intensive agricultural soils of Shanghai, China Li, Shuangxi; Li, Yujie; Hu, Cong Science of The Total Environment, Vol. 778 https://doi.org/10.1016/j.scitotenv.2021.146021	journal	July 2021
Generic concepts in Nectriaceae Lombard, L.; van der Merwe, N. A.; Groenewald, J. Z. Studies in Mycology, Vol. 80 https://doi.org/10.1016/j.simyco.2014.12.002	journal	March 2015
Didymellaceae revisited Chen, Q.; Hou, L. W.; Duan, W. J. Studies in Mycology, Vol. 87 https://doi.org/10.1016/j.simyco.2017.06.002	journal	June 2017
Predicting measures of soil health using the microbiome and supervised machine learning Wilhelm, Roland C.; van Es, Harold M.; Buckley, Daniel H. Soil Biology and Biochemistry, Vol. 164 https://doi.org/10.1016/j.soilbio.2021.108472	journal	January 2022
Tillage homogenizes soil bacterial communities in microaggregate fractions by facilitating dispersal West, Jaimie R.; Lauer, Joseph G.; Whitman, Thea Soil Biology and Biochemistry, Vol. 186 https://doi.org/10.1016/j.soilbio.2023.109181	journal	November 2023
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
Random Forests Breiman, Leo Machine Learning, Vol. 45, Issue 1, p. 5-32 https://doi.org/10.1023/A:1010933404324	journal	January 2001
Deterministic processes vary during community assembly for ecologically dissimilar taxa Powell, Jeff R.; Karunaratne, Senani; Campbell, Colin D. Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms9444	journal	October 2015
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
Microbial interactions: from networks to models Faust, Karoline; Raes, Jeroen Nature Reviews Microbiology, Vol. 10, Issue 8 https://doi.org/10.1038/nrmicro2832	journal	July 2012
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
Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China Jiao, Shuo; Yang, Yunfeng; Xu, Yiqin The ISME Journal, Vol. 14, Issue 1 https://doi.org/10.1038/s41396-019-0522-9	journal	October 2019
Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt Yuan, Jun; Wen, Tao; Zhang, He The ISME Journal, Vol. 14, Issue 12 https://doi.org/10.1038/s41396-020-0720-5	journal	July 2020
Open challenges for microbial network construction and analysis Faust, Karoline The ISME Journal, Vol. 15, Issue 11 https://doi.org/10.1038/s41396-021-01027-4	journal	June 2021
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
Top-down identification of keystone taxa in the microbiome Amit, Guy; Bashan, Amir Nature Communications, Vol. 14, Issue 1 https://doi.org/10.1038/s41467-023-39459-5	journal	July 2023
Climate warming enhances microbial network complexity and stability Yuan, Mengting Maggie; Guo, Xue; Wu, Linwei Nature Climate Change, Vol. 11, Issue 4 https://doi.org/10.1038/s41558-021-00989-9	journal	February 2021
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
Priority effects in microbiome assembly Debray, Reena; Herbert, Robin A.; Jaffe, Alexander L. Nature Reviews Microbiology, Vol. 20, Issue 2 https://doi.org/10.1038/s41579-021-00604-w	journal	August 2021
Machine learning for microbiologists Asnicar, Francesco; Thomas, Andrew Maltez; Passerini, Andrea Nature Reviews Microbiology, Vol. 22, Issue 4 https://doi.org/10.1038/s41579-023-00984-1	journal	November 2023
Metabolomic and microbiome profiling reveals personalized risk factors for coronary artery disease Talmor-Barkan, Yeela; Bar, Noam; Shaul, Aviv A. Nature Medicine, Vol. 28, Issue 2 https://doi.org/10.1038/s41591-022-01686-6	journal	February 2022
SciPy 1.0: fundamental algorithms for scientific computing in Python Virtanen, Pauli; Gommers, Ralf; Oliphant, Travis E. Nature Methods https://doi.org/10.1038/s41592-019-0686-2	journal	February 2020
Fungal community shifts in soils with varied cover crop treatments and edaphic properties Cloutier, Mara L.; Murrell, Ebony; Barbercheck, Mary Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-63173-7	journal	April 2020
From local explanations to global understanding with explainable AI for trees Lundberg, Scott M.; Erion, Gabriel; Chen, Hugh Nature Machine Intelligence, Vol. 2, Issue 1 https://doi.org/10.1038/s42256-019-0138-9	journal	January 2020
Machine learning and deep learning applications in microbiome research Hernández Medina, Ricardo; Kutuzova, Svetlana; Nielsen, Knud Nor ISME Communications, Vol. 2, Issue 1 https://doi.org/10.1038/s43705-022-00182-9	journal	October 2022
Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession Dini-Andreote, Francisco; Stegen, James C.; van Elsas, Jan Dirk Proceedings of the National Academy of Sciences, Vol. 112, Issue 11 https://doi.org/10.1073/pnas.1414261112	journal	March 2015
Depth-Dependent Patterns of Bacterial Communities and Assembly Processes in a Typical Red Soil Critical Zone Wu, Huayong; Adams, Jonathan M.; Shi, Yu Geomicrobiology Journal, Vol. 37, Issue 3 https://doi.org/10.1080/01490451.2019.1688432	journal	November 2019
Predicting microbiomes through a deep latent space García-Jiménez, Beatriz; Muñoz, Jorge; Cabello, Sara Bioinformatics, Vol. 37, Issue 10 https://doi.org/10.1093/bioinformatics/btaa971	journal	December 2020
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data Robinson, M. D.; McCarthy, D. J.; Smyth, G. K. Bioinformatics, Vol. 26, Issue 1 https://doi.org/10.1093/bioinformatics/btp616	journal	November 2009
Some distance properties of latent root and vector methods used in multivariate analysis Gower, J. C. Biometrika, Vol. 53, Issue 3-4 https://doi.org/10.1093/biomet/53.3-4.325	journal	January 1966
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB Pruesse, E.; Quast, C.; Knittel, K. Nucleic Acids Research, Vol. 35, Issue 21 https://doi.org/10.1093/nar/gkm864	journal	November 2007
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1219	journal	November 2012
Predators of Soil Bacteria in Plant and Human Health Martins, Samuel J.; Taerum, Stephen J.; Triplett, Lindsay Phytobiomes Journal, Vol. 6, Issue 3 https://doi.org/10.1094/PBIOMES-11-21-0073-RVW	journal	September 2022
Finding community structure in very large networks Clauset, Aaron; Newman, M. E. J.; Moore, Cristopher Physical Review E, Vol. 70, Issue 6 https://doi.org/10.1103/PhysRevE.70.066111	journal	December 2004
iForest: Interpreting Random Forests via Visual Analytics Zhao, Xun; Wu, Yanhong; Lee, Dik Lun IEEE Transactions on Visualization and Computer Graphics, Vol. 25, Issue 1 https://doi.org/10.1109/TVCG.2018.2864475	journal	January 2019
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
Spatial scale drives patterns in soil bacterial diversity: Spatial scale drives soil diversity O'Brien, Sarah L.; Gibbons, Sean M.; Owens, Sarah M. Environmental Microbiology, Vol. 18, Issue 6 https://doi.org/10.1111/1462-2920.13231	journal	March 2016
Machine learning and deep learning—A review for ecologists Pichler, Maximilian; Hartig, Florian Methods in Ecology and Evolution, Vol. 14, Issue 4 https://doi.org/10.1111/2041-210X.14061	journal	February 2023
Neutral theory and community ecology: Neutral theory and community ecology Chave, J. Ecology Letters, Vol. 7, Issue 3 https://doi.org/10.1111/j.1461-0248.2003.00566.x	journal	February 2004
Assembly history dictates ecosystem functioning: evidence from wood decomposer communities: Carbon dynamics and fungal community assembly Fukami, Tadashi; Dickie, Ian A.; Paula Wilkie, J. Ecology Letters, Vol. 13, Issue 6 https://doi.org/10.1111/j.1461-0248.2010.01465.x	journal	April 2010
Quantifying the roles of immigration and chance in shaping prokaryote community structure Sloan, William T.; Lunn, Mary; Woodcock, Stephen Environmental Microbiology, Vol. 8, Issue 4 https://doi.org/10.1111/j.1462-2920.2005.00956.x	journal	April 2006
Collinearity: a review of methods to deal with it and a simulation study evaluating their performance Dormann, Carsten F.; Elith, Jane; Bacher, Sven Ecography, Vol. 36, Issue 1 https://doi.org/10.1111/j.1600-0587.2012.07348.x	journal	May 2012
Improving indicator species analysis by combining groups of sites De Cáceres, Miquel; Legendre, Pierre; Moretti, Marco Oikos, Vol. 119, Issue 10 https://doi.org/10.1111/j.1600-0706.2010.18334.x	journal	September 2010
Local and regional factors influencing bacterial community assembly: Bacterial community assembly Lindström, Eva S.; Langenheder, Silke Environmental Microbiology Reports, Vol. 4, Issue 1 https://doi.org/10.1111/j.1758-2229.2011.00257.x	journal	April 2011
Cross-Validatory Choice and Assessment of Statistical Predictions Stone, M. Journal of the Royal Statistical Society: Series B (Methodological), Vol. 36, Issue 2 https://doi.org/10.1111/j.2517-6161.1974.tb00994.x	journal	January 1974
The fungal pathogen Corynespora cassiicola: A review and insights for target spot management on cotton and Soya bean N. Rondon, Marina; Lawrence, Kathy Journal of Phytopathology, Vol. 169, Issue 6 https://doi.org/10.1111/jph.12992	journal	March 2021
Application of multivariate statistical techniques in microbial ecology Paliy, O.; Shankar, V. Molecular Ecology, Vol. 25, Issue 5 https://doi.org/10.1111/mec.13536	journal	February 2016
Effects of cotton–maize rotation on soil microbiome structure Xi, Hui; Zhang, Xuekun; Qu, Zheng Molecular Plant Pathology, Vol. 22, Issue 6 https://doi.org/10.1111/mpp.13053	journal	March 2021
Controls on Diatom Biogeography in the Ocean Cermeno, P.; Falkowski, P. G. Science, Vol. 325, Issue 5947 https://doi.org/10.1126/science.1174159	journal	September 2009
Determinants of community structure in the global plankton interactome Lima-Mendez, G.; Faust, K.; Henry, N. Science, Vol. 348, Issue 6237 https://doi.org/10.1126/science.1262073	journal	May 2015
Modeling Macroscopic Patterns in Ecology Enquist, B. J. Science, Vol. 295, Issue 5561 https://doi.org/10.1126/science.295.5561.1835c	journal	March 2002
The Effects of Soil Depth on the Structure of Microbial Communities in Agricultural Soils in Iowa (United States) Hao, Jingjie; Chai, Yen Ning; Lopes, Lucas Dantas Applied and Environmental Microbiology, Vol. 87, Issue 4 https://doi.org/10.1128/AEM.02673-20	journal	January 2021
Characterization of an Atrazine-DegradingPseudaminobactersp. Isolated from Canadian and French Agricultural Soils Topp, Edward; Zhu, Hong; Nour, Sarah M. Applied and Environmental Microbiology, Vol. 66, Issue 7 https://doi.org/10.1128/AEM.66.7.2773-2782.2000	journal	July 2000
Responses of Active Bacterial and Fungal Communities in Soils under Winter Wheat to Different Fertilizer and Pesticide Regimens Girvan, Martina S.; Bullimore, Juliet; Ball, Andrew S. Applied and Environmental Microbiology, Vol. 70, Issue 5 https://doi.org/10.1128/AEM.70.5.2692-2701.2004	journal	May 2004
Microbiome Aggregated Traits and Assembly Are More Sensitive to Soil Management than Diversity Neal, Andrew L.; Hughes, David; Clark, Ian M. mSystems, Vol. 6, Issue 3 https://doi.org/10.1128/mSystems.01056-20	journal	June 2021
Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks DiMucci, Demetrius; Kon, Mark; Segrè, Daniel mSystems, Vol. 3, Issue 5 https://doi.org/10.1128/msystems.00181-18	journal	October 2018
Coupling Bacterial Community Assembly to Microbial Metabolism across Soil Profiles Luan, Lu; Liang, Chao; Chen, Lijun mSystems, Vol. 5, Issue 3 https://doi.org/10.1128/msystems.00298-20	journal	June 2020
Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data Armstrong, George; Martino, Cameron; Rahman, Gibraan mSystems, Vol. 6, Issue 5 https://doi.org/10.1128/msystems.00691-21	journal	October 2021
"Why Should I Trust You?": Explaining the Predictions of Any Classifier Ribeiro, Marco Tulio; Singh, Sameer; Guestrin, Carlos Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining - KDD '16 https://doi.org/10.1145/2939672.2939778	conference	January 2016
Leveraging explainable AI for gut microbiome-based colorectal cancer classification Rynazal, Ryza; Fujisawa, Kota; Shiroma, Hirotsugu Genome Biology, Vol. 24, Issue 1 https://doi.org/10.1186/s13059-023-02858-4	journal	February 2023
Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection Montassier, Emmanuel; Al-Ghalith, Gabriel A.; Ward, Tonya Genome Medicine, Vol. 8, Issue 1 https://doi.org/10.1186/s13073-016-0301-4	journal	April 2016
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
Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data Davis, Nicole M.; Proctor, Diana M.; Holmes, Susan P. Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0605-2	journal	December 2018
Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons Chen, Weidong; Ren, Kexin; Isabwe, Alain Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0749-8	journal	October 2019
Earth microbial co-occurrence network reveals interconnection pattern across microbiomes Ma, Bin; Wang, Yiling; Ye, Shudi Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-00857-2	journal	June 2020
Predicting microbial community compositions in wastewater treatment plants using artificial neural networks Liu, Xiaonan; Nie, Yong; Wu, Xiao-Lei Microbiome, Vol. 11, Issue 1 https://doi.org/10.1186/s40168-023-01519-9	journal	April 2023
Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation Agler, Matthew T.; Ruhe, Jonas; Kroll, Samuel PLOS Biology, Vol. 14, Issue 1 https://doi.org/10.1371/journal.pbio.1002352	journal	January 2016
Novel Covariance-Based Neutrality Test of Time-Series Data Reveals Asymmetries in Ecological and Economic Systems Washburne, Alex D.; Burby, Joshua W.; Lacker, Daniel PLOS Computational Biology, Vol. 12, Issue 9 https://doi.org/10.1371/journal.pcbi.1005124	journal	September 2016
Structure, Composition and Metagenomic Profile of Soil Microbiomes Associated to Agricultural Land Use and Tillage Systems in Argentine Pampas Carbonetto, Belén; Rascovan, Nicolás; Álvarez, Roberto PLoS ONE, Vol. 9, Issue 6 https://doi.org/10.1371/journal.pone.0099949	journal	June 2014
A Value for n-Person Games Shapley, L. S. Contributions to the Theory of Games (AM-28), Vol. 2 https://doi.org/10.1515/9781400881970-018	book	December 1953
UNITE general FASTA release for Fungi Abarenkov, Kessy; Zirk, Allan; Piirmann, Timo UNITE Community https://doi.org/10.15156/BIO/2959332	dataset	January 2024
Effects of agricultural management on soil organic matter and carbon transformation - a review Liu, X.; Herbert, S. J.; Hashemi, A. M. Plant, Soil and Environment, Vol. 52, Issue 12 https://doi.org/10.17221/3544-PSE	journal	December 2006
Distance-Based Redundancy Analysis: Testing Multispecies Responses in Multifactorial Ecological Experiments Legendre, Pierre; Anderson, Marti J. Ecological Monographs, Vol. 69, Issue 1 https://doi.org/10.1890/0012-9615(1999)069[0001:DBRATM]2.0.CO;2	journal	February 1999
Biological Communities as Functionally Organized Units Wilson, David Sloan Ecology, Vol. 78, Issue 7 https://doi.org/10.1890/0012-9658(1997)078[2018:BCAFOU]2.0.CO;2	journal	October 1997
Soil biota community structure and abundance under agricultural intensification and extensification Postma-Blaauw, Maria B.; de Goede, Ron G. M.; Bloem, Jaap Ecology, Vol. 91, Issue 2 https://doi.org/10.1890/09-0666.1	journal	February 2010
Ecological determinism increases with organism size Farjalla, Vinicius F.; Srivastava, Diane S.; Marino, Nicholas A. C. Ecology, Vol. 93, Issue 7 https://doi.org/10.1890/11-1144.1	journal	July 2012
Soil Structural Disturbance Effects on Crop Yields and Soil Properties in a No‐Till Production System Díaz‐Zorita, M.; Grove, J. H.; Murdock, L. Agronomy Journal, Vol. 96, Issue 6 https://doi.org/10.2134/agronj2004.1651	journal	November 2004
Taxonomy, phylogeny and identification of Chaetomiaceae with emphasis on thermophilic species Wang, X. W.; Han, P. J.; Bai, F. Y. Studies in Mycology, Vol. 101, Issue 1 https://doi.org/10.3114/sim.2022.101.03	journal	March 2022
Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton Apprill, A.; McNally, S.; Parsons, R. Aquatic Microbial Ecology, Vol. 75, Issue 2 https://doi.org/10.3354/ame01753	journal	June 2015
Deciphering microbial interactions and detecting keystone species with co-occurrence networks Berry, David; Widder, Stefanie Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00219	journal	May 2014
Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes Degrune, Florine; Theodorakopoulos, Nicolas; Colinet, Gilles Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01127	journal	June 2017
Microbial Communities Associated With Long-Term Tillage and Fertility Treatments in a Corn-Soybean Cropping System Srour, Ali Y.; Ammar, Hala A.; Subedi, Arjun Frontiers in Microbiology, Vol. 11 https://doi.org/10.3389/fmicb.2020.01363	journal	June 2020
Biogeography and Ecology of Magnaporthales: A Case Study Feng, Jia-Wei; Liu, Wei-Ting; Chen, Jia-Jie Frontiers in Microbiology, Vol. 12 https://doi.org/10.3389/fmicb.2021.654380	journal	May 2021
Dispersal Limitation Plays Stronger Role in the Community Assembly of Fungi Relative to Bacteria in Rhizosphere Across the Arable Area of Medicinal Plant Zhang, Guozhuang; Wei, Guangfei; Wei, Fugang Frontiers in Microbiology, Vol. 12 https://doi.org/10.3389/fmicb.2021.713523	journal	August 2021
The Shift of Soil Bacterial Community After Afforestation Influence Soil Organic Carbon and Aggregate Stability in Karst Region Lan, Jiacheng; Wang, Shasha; Wang, Junxian Frontiers in Microbiology, Vol. 13 https://doi.org/10.3389/fmicb.2022.901126	journal	June 2022
Microbiome as a Key Player in Sustainable Agriculture and Human Health Suman, Jarupula; Rakshit, Amitava; Ogireddy, Siva Devika Frontiers in Soil Science, Vol. 2 https://doi.org/10.3389/fsoil.2022.821589	journal	April 2022
Advances in Eco-Efficient Agriculture: The Plant-Soil Mycobiome Pagano, Marcela; Correa, Eduardo; Duarte, Neimar Agriculture, Vol. 7, Issue 2 https://doi.org/10.3390/agriculture7020014	journal	February 2017
Fertilization and Soil Microbial Community: A Review Dincă, Lucian Constantin; Grenni, Paola; Onet, Cristian Applied Sciences, Vol. 12, Issue 3 https://doi.org/10.3390/app12031198	journal	January 2022
Species Diversity, Distribution, and Phylogeny of Exophiala with the Addition of Four New Species from Thailand Thitla, Tanapol; Kumla, Jaturong; Khuna, Surapong Journal of Fungi, Vol. 8, Issue 8 https://doi.org/10.3390/jof8080766	journal	July 2022

Similar Records

Microbiome Aggregated Traits and Assembly Are More Sensitive to Soil Management than Diversity

Journal Article · 2021 · mSystems · OSTI ID:1813588

Neal, Andrew L.; Hughes, David; Clark, Ian M.; +2 more

Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture

Journal Article · 2020 · Frontiers in Microbiology · OSTI ID:1737691

Ray, Prasun; Lakshmanan, Venkatachalam; Labbé, Jessy L.; +1 more

Modeling biogeochemistry in agricultural soils

Journal Article · 1994 · Global Biogeochemical Cycles · OSTI ID:96048

Li, C; Frolking, S; Harriss, R

Related Subjects

60 APPLIED LIFE SCIENCES
Agriculture
Microbial ecology
Soil microbiology

Title: Agricultural practices influence soil microbiome assembly and interactions at different depths identified by machine learning

Citation Formats

References (106)

Similar Records

Related Subjects