Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome.
metagenomics
microbial community
nitrogen fixation
soil microbiome
Journal
Microbiome
ISSN: 2049-2618
Titre abrégé: Microbiome
Pays: England
ID NLM: 101615147
Informations de publication
Date de publication:
24 May 2024
24 May 2024
Historique:
received:
28
04
2023
accepted:
09
04
2024
medline:
25
5
2024
pubmed:
25
5
2024
entrez:
24
5
2024
Statut:
epublish
Résumé
Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments). Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.
Sections du résumé
BACKGROUND
BACKGROUND
Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N
RESULTS
RESULTS
After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments).
CONCLUSION
CONCLUSIONS
Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.
Identifiants
pubmed: 38790049
doi: 10.1186/s40168-024-01812-1
pii: 10.1186/s40168-024-01812-1
doi:
Substances chimiques
Soil
0
Nitrogen
N762921K75
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
95Informations de copyright
© 2024. The Author(s).
Références
Vitousek PM, Cassman K, Cleveland C, Crews T, Field CB, Grimm NB, et al. Towards an ecological understanding of biological nitrogen fixation. Biogeochemistry. 2002;57:1–45. https://doi.org/10.1023/A:1015798428743 .
doi: 10.1023/A:1015798428743
Beijerinck MW. Die bacterien der papilionaceenknöllchen. Botanische Zeitung. 1888;46:725–35.
Bürgmann H, Widmer F, Von Sigler W, Zeyer J. New Molecular Screening Tools for Analysis of Free-Living Diazotrophs in Soil. Appl Environ Microbiol. 2004;70:240–7. https://doi.org/10.1128/AEM.70.1.240-247.2004 .
doi: 10.1128/AEM.70.1.240-247.2004
pubmed: 14711647
pmcid: 321232
Hsu S-F, Buckley DH. Evidence for the functional significance of diazotroph community structure in soil. The ISME Journal. 2009;3:124–36. https://doi.org/10.1038/ismej.2008.82 .
doi: 10.1038/ismej.2008.82
pubmed: 18769458
Nelson MB, Martiny AC, Martiny JBH. Global biogeography of microbial nitrogen-cycling traits in soil. Proc Natl Acad Sci. 2016;113:8033–40. https://doi.org/10.1073/pnas.1601070113 .
doi: 10.1073/pnas.1601070113
pubmed: 27432978
pmcid: 4961168
Dos Santos PC, Fang Z, Mason SW, Setubal JC, Dixon R. Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes. BMC Genomics. 2012;13:162. https://doi.org/10.1186/1471-2164-13-162 .
doi: 10.1186/1471-2164-13-162
pubmed: 22554235
pmcid: 3464626
Che R, Deng Y, Wang F, Wang W, Xu Z, Hao Y, et al. Autotrophic and symbiotic diazotrophs dominate nitrogen-fixing communities in Tibetan grassland soils. Sci Total Environ. 2018;639:997–1006. https://doi.org/10.1016/j.scitotenv.2018.05.238 .
doi: 10.1016/j.scitotenv.2018.05.238
pubmed: 29929338
Gaby JC, Buckley DH. A global census of nitrogenase diversity. Environ Microbiol. 2011;13:1790–9. https://doi.org/10.1111/j.1462-2920.2011.02488.x .
doi: 10.1111/j.1462-2920.2011.02488.x
pubmed: 21535343
Wang Q, Quensen JF, Fish JA, Kwon Lee T, Sun Y, Tiedje JM, et al. Ecological Patterns of nifH Genes in Four Terrestrial Climatic Zones Explored with Targeted Metagenomics Using FrameBot, a New Informatics Tool. mBio. 2013;4. https://doi.org/10.1128/mBio.00592-13 .
Yu Y, Zhang J, Petropoulos E, Baluja MQ, Zhu C, Zhu J, et al. Divergent Responses of the Diazotrophic Microbiome to Elevated CO
Zhu C, Friman V, Li L, Xu Q, Guo J, Guo S, et al. Meta-analysis of diazotrophic signatures across terrestrial ecosystems at the continental scale. Environ Microbiol. 2022;24:2013–28. https://doi.org/10.1111/1462-2920.15984 .
doi: 10.1111/1462-2920.15984
pubmed: 35362656
Kuypers MMM, Marchant HK, Kartal B. The microbial nitrogen-cycling network. Nat Rev Microbiol. 2018;16:263–76. https://doi.org/10.1038/nrmicro.2018.9 .
doi: 10.1038/nrmicro.2018.9
pubmed: 29398704
Mahmud K, Makaju S, Ibrahim R, Missaoui A. Current Progress in Nitrogen Fixing Plants and Microbiome Research. Plants. 2020;9:97. https://doi.org/10.3390/plants9010097 .
doi: 10.3390/plants9010097
pubmed: 31940996
pmcid: 7020401
Masuda Y, Itoh H, Shiratori Y, Isobe K, Otsuka S, Senoo K. Predominant but previously-overlooked prokaryotic drivers of reductive nitrogen transformation in paddy soils, revealed by metatranscriptomics. Microbes Environ. 2017;32:180–3. https://doi.org/10.1264/jsme2.ME16179 .
doi: 10.1264/jsme2.ME16179
pubmed: 28442658
pmcid: 5478542
Calderoli PA, Collavino MM, Behrends Kraemer F, Morrás HJM, Aguilar OM. Analysis of nifH-RNA reveals phylotypes related to Geobacter and Cyanobacteria as important functional components of the N
Fan K, Delgado-Baquerizo M, Guo X, Wang D, Wu Y, Zhu M, et al. Suppressed N fixation and diazotrophs after four decades of fertilization. Microbiome. 2019;7:143. https://doi.org/10.1186/s40168-019-0757-8 .
doi: 10.1186/s40168-019-0757-8
pubmed: 31672173
pmcid: 6824023
Feng M, Adams JM, Fan K, Shi Y, Sun R, Wang D, et al. Long-term fertilization influences community assembly processes of soil diazotrophs. Soil Biol Biochem. 2018;126:151–8. https://doi.org/10.1016/j.soilbio.2018.08.021 .
doi: 10.1016/j.soilbio.2018.08.021
Wang C, Zheng MM, Chen J, Shen RF. Land-use change has a greater effect on soil diazotrophic community structure than the plant rhizosphere in acidic ferralsols in southern China. Plant Soil. 2021a;462:445–58. https://doi.org/10.1007/s11104-021-04883-3 .
doi: 10.1007/s11104-021-04883-3
Mitter EK, Germida JJ, de Freitas JR. Impact of diesel and biodiesel contamination on soil microbial community activity and structure. Sci Rep. 2021;11:10856. https://doi.org/10.1038/s41598-021-89637-y .
doi: 10.1038/s41598-021-89637-y
pubmed: 34035323
pmcid: 8149423
Pecher WT, Martínez FL, DasSarma P, Guzmán D, DasSarma S. 16S rRNA Gene Diversity in Ancient Gray and Pink Salt from San Simón Salt Mines in Tarija, Bolivia. Microbiology Resource Announcements. 2020;9:e00820–0. https://doi.org/10.1128/MRA.00820-20 .
doi: 10.1128/MRA.00820-20
pubmed: 33033125
pmcid: 7545279
Sun W, Xiao E, Pu Z, Krumins V, Dong Y, Li B, et al. Paddy soil microbial communities driven by environment- and microbe-microbe interactions: A case study of elevation-resolved microbial communities in a rice terrace. Sci Total Environ. 2018;612:884–93. https://doi.org/10.1016/j.scitotenv.2017.08.275 .
doi: 10.1016/j.scitotenv.2017.08.275
pubmed: 28886540
Weber KA, Achenbach LA, Coates JD. Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction. Nat Rev Microbiol. 2006;4:752–64. https://doi.org/10.1038/nrmicro1490 .
doi: 10.1038/nrmicro1490
pubmed: 16980937
Itoh H, Xu Z, Masuda Y, Ushijima N, Hayakawa C, Shiratori Y, et al. Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas. Int J Syst Evol Microbiol. 2021;71:004607. https://doi.org/10.1099/ijsem.0.004607 .
Itoh H, Xu Z, Mise K, Masuda Y, Ushijima N, Hayakawa C, et al. Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov., isolated from paddy soils. Int J Syst Evol Microbiol. 2022;72:005546. https://doi.org/10.1099/ijsem.0.005546 .
doi: 10.1099/ijsem.0.005546
Liu G-H, Yang S, Tang R, Xie C-J, Zhou S-G. Genome Analysis and Description of Three Novel Diazotrophs Geomonas Species Isolated From Paddy Soils. Front Microbiol. 2021;12:801462. https://doi.org/10.3389/fmicb.2021.801462 .
doi: 10.3389/fmicb.2021.801462
pubmed: 35197944
Masuda Y, Yamanaka H, Xu Z-X, Shiratori Y, Aono T, Amachi S, et al. Diazotrophic Anaeromyxobacter Isolates from Soils. Appl Environ Microbiol. 2020;86:e00956–20. https://doi.org/10.1128/AEM.00956-20 .
doi: 10.1128/AEM.00956-20
pubmed: 32532868
pmcid: 7414960
Xu Z, Masuda Y, Hayakawa C, Ushijima N, Kawano K, Shiratori Y, et al. Description of Three Novel Members in the Family Geobacteraceae, Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov. Microorganisms. 2020;8:634. https://doi.org/10.3390/microorganisms8050634 .
doi: 10.3390/microorganisms8050634
pubmed: 32349406
pmcid: 7285026
Xu Z, Masuda Y, Itoh H, Ushijima N, Shiratori Y, Senoo K. Geomonas oryzae gen. nov., sp. nov., Geomonas edaphica sp. nov., Geomonas ferrireducens sp. nov., Geomonas terrae sp. nov., Four Ferric-Reducing Bacteria Isolated From Paddy Soil, and Reclassification of Three Species of the Genus Geobacter as Members of the Genus Geomonas gen. nov. Front Microbiol. 2019;10:2201. https://doi.org/10.3389/fmicb.2019.02201 .
doi: 10.3389/fmicb.2019.02201
pubmed: 31608033
pmcid: 6773877
Xu Z, Masuda Y, Wang X, Ushijima N, Shiratori Y, Senoo K, et al. Genome-Based Taxonomic Rearrangement of the Order Geobacterales Including the Description of Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov. Front Microbiol. 2021;12:2715. https://doi.org/10.3389/fmicb.2021.737531 .
doi: 10.3389/fmicb.2021.737531
Yang S, Liu G-H, Tang R, Han S, Xie C-J, Zhou S-G. Description of two nitrogen-fixing bacteria, Geomonas fuzhouensis sp. nov. and Geomonas agri sp. nov., isolated from paddy soils. Antonie Van Leeuwenhoek. 2022;115:435–44. https://doi.org/10.1007/s10482-021-01704-6 .
doi: 10.1007/s10482-021-01704-6
pubmed: 35094155
Zhang Z, Xu Z, Masuda Y, Wang X, Ushijima N, Shiratori Y, et al. Geomesophilobacter sediminis gen. nov., sp. nov., Geomonas propionica sp. nov. and Geomonas anaerohicana sp. nov., three novel members in the family Geobacterecace isolated from river sediment and paddy soil. Syst Appl Microbiol. 2021;44:126233. https://doi.org/10.1016/j.syapm.2021.126233 .
doi: 10.1016/j.syapm.2021.126233
pubmed: 34311149
Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, et al. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol. 2018;3:804–13. https://doi.org/10.1038/s41564-018-0176-9 .
doi: 10.1038/s41564-018-0176-9
pubmed: 29891866
pmcid: 6792437
Jones CM, Graf DR, Bru D, Philippot L, Hallin S. The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink. The ISME Journal. 2013;7:417–26. https://doi.org/10.1038/ismej.2012.125 .
doi: 10.1038/ismej.2012.125
pubmed: 23151640
Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, et al. Target-enrichment strategies for next-generation sequencing. Nat Methods. 2010;7:111–8. https://doi.org/10.1038/nmeth.1419 .
doi: 10.1038/nmeth.1419
pubmed: 20111037
Mamedov TG, Pienaar E, Whitney SE, TerMaat JR, Carvill G, Goliath R, et al. A fundamental study of the PCR amplification of GC-rich DNA templates. Comput Biol Chem. 2008;32:452–7. https://doi.org/10.1016/j.compbiolchem.2008.07.021 .
doi: 10.1016/j.compbiolchem.2008.07.021
pubmed: 18760969
Mise K, Masuda Y, Senoo K, Itoh H. Undervalued Pseudo-nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers. mSphere. 2021;6:e00785–21. https://doi.org/10.1128/msphere.00785-21 .
doi: 10.1128/msphere.00785-21
pubmed: 34787447
pmcid: 8597730
Strien J, Sanft J, Mall G. Enhancement of PCR Amplification of Moderate GC-Containing and Highly GC-Rich DNA Sequences. Mol Biotechnol. 2013;54:1048–54. https://doi.org/10.1007/s12033-013-9660-x .
doi: 10.1007/s12033-013-9660-x
pubmed: 23568183
Gaby JC, Buckley DH. A comprehensive evaluation of PCR primers to amplify the nifH gene of nitrogenase. PLoS One. 2012;9:e93883. https://doi.org/10.1371/journal.pone.0042149 .
doi: 10.1371/journal.pone.0042149
Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014;64:346–51. https://doi.org/10.1099/ijs.0.059774-0 .
doi: 10.1099/ijs.0.059774-0
pubmed: 24505072
Bazylinski DA, Dean AJ, Schuler D, Phillips EJP, Lovley DR. N
doi: 10.1046/j.1462-2920.2000.00096.x
pubmed: 11200427
Katz K, Shutov O, Lapoint R, Kimelman M, Brister JR, O’Sullivan C. The Sequence Read Archive: a decade more of explosive growth. Nucleic Acids Res. 2022;50:D387–90. https://doi.org/10.1093/nar/gkab1053 .
doi: 10.1093/nar/gkab1053
pubmed: 34850094
Meyer F, Bagchi S, Chaterji S, Gerlach W, Grama A, Harrison T, et al. MG-RAST version 4—lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis. Brief Bioinform. 2019;20:1151–9. https://doi.org/10.1093/bib/bbx105 .
doi: 10.1093/bib/bbx105
pubmed: 29028869
Mus F, Alleman AB, Pence N, Seefeldt LC, Peters JW. Exploring the alternatives of biological nitrogen fixation. Metallomics. 2018;10:523–38. https://doi.org/10.1039/C8MT00038G .
doi: 10.1039/C8MT00038G
pubmed: 29629463
Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil P-A, Hugenholtz P. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res. 2022;50:D785–94. https://doi.org/10.1093/nar/gkab776 .
doi: 10.1093/nar/gkab776
pubmed: 34520557
Robson RL, Postgate JR. Oxygen and Hydrogen in Biological Nitrogen Fixation. Ann Rev Microbiol. 1980;34:183–207. https://doi.org/10.1146/annurev.mi.34.100180.001151 .
doi: 10.1146/annurev.mi.34.100180.001151
Zhou J, Ma M, Guan D, Jiang X, Zhang N, Shu F, et al. Nitrogen has a greater influence than phosphorus on the diazotrophic community in two successive crop seasons in Northeast China. Sci Rep. 2021;11:6303. https://doi.org/10.1038/s41598-021-85829-8 .
doi: 10.1038/s41598-021-85829-8
pubmed: 33737649
pmcid: 7973567
Wang H, He X, Zhang Z, Li M, Zhang Q, Zhu H, et al. Eight years of manure fertilization favor copiotrophic traits in paddy soil microbiomes. Eur J Soil Biol. 2021b;106:103352. https://doi.org/10.1016/j.ejsobi.2021.103352 .
doi: 10.1016/j.ejsobi.2021.103352
Drake JB, Weishampel JF. Multifractal analysis of canopy height measures in a longleaf pine savanna. For Ecol Manag. 2000;128:121–7. https://doi.org/10.1016/S0378-1127(99)00279-0 .
doi: 10.1016/S0378-1127(99)00279-0
Pi H-W, Lin J-J, Chen C-A, Wang P-H, Chiang Y-R, Huang C-C, et al. Origin and Evolution of Nitrogen Fixation in Prokaryotes. Molecular Biology and Evolution 39, msac181. 2022; https://doi.org/10.1093/molbev/msac181 .
Raymond J, Siefert JL, Staples CR, Blankenship RE. The Natural History of Nitrogen Fixation. Mol Biol Evol. 2004;21:541–54. https://doi.org/10.1093/molbev/msh047 .
doi: 10.1093/molbev/msh047
pubmed: 14694078
Brown JR. Ancient horizontal gene transfer. Nat Rev Genet. 2003;4:121–32. https://doi.org/10.1038/nrg1000 .
doi: 10.1038/nrg1000
pubmed: 12560809
Wang H, Li X, Li X, Li F, Su Z, Zhang H. Community Composition and Co-Occurrence Patterns of Diazotrophs along a Soil Profile in Paddy Fields of Three Soil Types in China. Microb Ecol. 2021c;82:961–70. https://doi.org/10.1007/s00248-021-01716-9 .
doi: 10.1007/s00248-021-01716-9
pubmed: 33660069
Nemergut DR, Schmidt SK, Fukami T, O’Neill SP, Bilinski TM, Stanish LF, et al. Patterns and Processes of Microbial Community Assembly. Microbiol Mol Biol Rev. 2013;77:342–56. https://doi.org/10.1128/MMBR.00051-12 .
doi: 10.1128/MMBR.00051-12
pubmed: 24006468
pmcid: 3811611
Vellend M. Conceptual Synthesis in Community Ecology. Q Rev Biol. 2010;85:183–206. https://doi.org/10.1086/652373 .
doi: 10.1086/652373
pubmed: 20565040
Fodelianakis S, Valenzuela-Cuevas A, Barozzi A, Daffonchio D. Direct quantification of ecological drift at the population level in synthetic bacterial communities. The ISME Journal. 2021;15:55–66. https://doi.org/10.1038/s41396-020-00754-4 .
doi: 10.1038/s41396-020-00754-4
pubmed: 32855435
Xu X, Thornton PE, Post WM. A global analysis of soil microbial biomass carbon, nitrogen and phosphorus in terrestrial ecosystems. Glob Ecol Biogeogr. 2013;22:737–49. https://doi.org/10.1111/geb.12029 .
doi: 10.1111/geb.12029
Davidson NC, Fluet-Chouinard E, Finlayson CM. Global extent and distribution of wetlands: trends and issues. Mar Freshw Res. 2018;69:620. https://doi.org/10.1071/MF17019 .
doi: 10.1071/MF17019
Wang X, Teng Y, Ren W, Li Y, Yang T, Chen Y, et al. Variations of Bacterial and Diazotrophic Community Assemblies throughout the Soil Profile in Distinct Paddy Soil Types and Their Contributions to Soil Functionality. mSystems. 2022;7:e01047–21. https://doi.org/10.1128/msystems.01047-21 .
doi: 10.1128/msystems.01047-21
pubmed: 35229646
pmcid: 8941939
Abellan-Schneyder I, Matchado MS, Reitmeier S, Sommer A, Sewald Z, Baumbach J, et al. Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing. mSphere. 2021;6:e01202–20. https://doi.org/10.1128/mSphere.01202-20 .
doi: 10.1128/mSphere.01202-20
pubmed: 33627512
pmcid: 8544895
Kim DD, Park D, Yoon H, Yun T, Song MJ, Yoon S. Quantification of nosZ genes and transcripts in activated sludge microbiomes with novel group-specific qPCR methods validated with metagenomic analyses. Water Res. 2020;185:116261. https://doi.org/10.1016/j.watres.2020.116261 .
doi: 10.1016/j.watres.2020.116261
pubmed: 32791454
Aird D, Ross MG, Chen W-S, Danielsson M, Fennell T, Russ C, et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 2011;12:R18. https://doi.org/10.1186/gb-2011-12-2-r18 .
doi: 10.1186/gb-2011-12-2-r18
pubmed: 21338519
pmcid: 3188800
Sato MP, Ogura Y, Nakamura K, Nishida R, Gotoh Y, Hayashi M, et al. Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes. DNA Res. 2019;26:391–8. https://doi.org/10.1093/dnares/dsz017 .
doi: 10.1093/dnares/dsz017
pubmed: 31364694
pmcid: 6796507
Sevim V, Lee J, Egan R, Clum A, Hundley H, Lee J, et al. Shotgun metagenome data of a defined mock community using Oxford Nanopore. PacBio and Illumina technologies Scientific Data. 2019;6:285. https://doi.org/10.1038/s41597-019-0287-z .
doi: 10.1038/s41597-019-0287-z
pubmed: 31772173
Soumare A, Diedhiou AG, Thuita M, Hafidi M, Ouhdouch Y, Gopalakrishnan S, et al. Exploiting Biological Nitrogen Fixation: A Route Towards a Sustainable Agriculture. Plants. 2020;9:1011. https://doi.org/10.3390/plants9081011 .
doi: 10.3390/plants9081011
pubmed: 32796519
pmcid: 7464700
Masuda Y, Shiratori Y, Ohba H, Ishida T, Takano R, Satoh S, et al. Enhancement of the nitrogen-fixing activity of paddy soils owing to iron application. Soil Sci Plant Nutr. 2021;67:243–7. https://doi.org/10.1080/00380768.2021.1888629 .
doi: 10.1080/00380768.2021.1888629
Shen W, Long Y, Qiu Z, Gao N, Masuda Y, Itoh H, et al. Investigation of Rice Yields and Critical N Losses from Paddy Soil under Different N Fertilization Rates with Iron Application. Int J Environ Res Public Health. 2022;19:8707. https://doi.org/10.3390/ijerph19148707 .
doi: 10.3390/ijerph19148707
pubmed: 35886559
pmcid: 9318169
Choi J, Yang F, Stepanauskas R, Cardenas E, Garoutte A, Williams R, et al. Strategies to improve reference databases for soil microbiomes. The ISME Journal. 2017;11:829–34. https://doi.org/10.1038/ismej.2016.168 .
doi: 10.1038/ismej.2016.168
pubmed: 27935589
Dash B, Nayak S, Pahari A, Nayak SK. Verrucomicrobia in Soil: An Agricultural Perspective. In: Frontiers in Soil and Environmental Microbiology. CRC Press; 2020. p. 37–46. https://doi.org/10.1201/9780429485794-4 .
doi: 10.1201/9780429485794-4
Kielak AM, Barreto CC, Kowalchuk GA, van Veen JA, Kuramae EE. The Ecology of Acidobacteria: Moving beyond Genes and Genomes. Front Microbiol. 2016;7:744. https://doi.org/10.3389/fmicb.2016.00744 .
doi: 10.3389/fmicb.2016.00744
pubmed: 27303369
pmcid: 4885859
Zhang Z, Masuda Y, Xu Z, Shiratori Y, Ohba H, Senoo K. Active nitrogen fixation by iron-reducing bacteria in rice paddy soil and its further enhancement by iron application. Appl Sci. 2023;13:8156. https://doi.org/10.3390/app13148156 .
doi: 10.3390/app13148156
Coates JD, Phillips EJ, Lonergan DJ, Jenter H, Lovley DR. Isolation of Geobacter species from diverse sedimentary environments. Appl Environ Microbiol. 1996;62:1531–6. https://doi.org/10.1128/aem.62.5.1531-1536.1996 .
doi: 10.1128/aem.62.5.1531-1536.1996
pubmed: 8633852
pmcid: 167928
Lovley DR, Giovannoni SJ, White DC, Champine JE, Phillips EJP, Gorby YA, et al. Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. Arch Microbiol. 1993;159:336–44. https://doi.org/10.1007/BF00290916 .
doi: 10.1007/BF00290916
pubmed: 8387263
Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–9. https://doi.org/10.1101/gr.074492.107 .
doi: 10.1101/gr.074492.107
pubmed: 18349386
pmcid: 2336801
Kanehisa M, Furumichi M, Sato Y, Ishiguro-Watanabe M, Tanabe M. KEGG: Integrating viruses and cellular organisms. Nucleic Acids Res. 2021;49:D545–51. https://doi.org/10.1093/nar/gkaa970 .
doi: 10.1093/nar/gkaa970
pubmed: 33125081
Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119. https://doi.org/10.1186/1471-2105-11-119 .
doi: 10.1186/1471-2105-11-119
pubmed: 20211023
pmcid: 2848648
Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, Goto S, et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics. 2020;36:2251–2. https://doi.org/10.1093/bioinformatics/btz859 .
doi: 10.1093/bioinformatics/btz859
pubmed: 31742321
Katoh K. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–66. https://doi.org/10.1093/nar/gkf436 .
doi: 10.1093/nar/gkf436
pubmed: 12136088
pmcid: 135756
Price MN, Dehal PS, Arkin AP. FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments. PLoS One. 2010;5:e9490. https://doi.org/10.1371/journal.pone.0009490 .
doi: 10.1371/journal.pone.0009490
pubmed: 20224823
pmcid: 2835736
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2019;36:1925–7. https://doi.org/10.1093/bioinformatics/btz848 .
doi: 10.1093/bioinformatics/btz848
pubmed: 31730192
pmcid: 7703759
Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011;7:e1002195. https://doi.org/10.1371/journal.pcbi.1002195 .
doi: 10.1371/journal.pcbi.1002195
pubmed: 22039361
pmcid: 3197634
Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat Microbiol. 2016;1:16048. https://doi.org/10.1038/nmicrobiol.2016.48 .
doi: 10.1038/nmicrobiol.2016.48
pubmed: 27572647
Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021;49:W293–6. https://doi.org/10.1093/nar/gkab301 .
doi: 10.1093/nar/gkab301
pubmed: 33885785
pmcid: 8265157
Takada-Hoshino Y, Matsumoto N. An Improved DNA Extraction Method Using Skim Milk from Soils That Strongly Adsorb DNA. Microbes Environ. 2004;19:13–9. https://doi.org/10.1264/jsme2.19.13 .
doi: 10.1264/jsme2.19.13
Arita M, Karsch-Mizrachi I, Cochrane G. The international nucleotide sequence database collaboration. Nucleic Acids Res. 2021;49:D121–4. https://doi.org/10.1093/nar/gkaa967 .
doi: 10.1093/nar/gkaa967
pubmed: 33166387
Meyer F, Paarmann D, D’Souza M, Olson R, Glass E, Kubal M, et al. The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9:386. https://doi.org/10.1186/1471-2105-9-386 .
doi: 10.1186/1471-2105-9-386
pubmed: 18803844
pmcid: 2563014
Zhalnina K, Louie KB, Hao Z, Mansoori N, da Rocha UN, Shi S, et al. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol. 2018;3:470–80. https://doi.org/10.1038/s41564-018-0129-3 .
doi: 10.1038/s41564-018-0129-3
pubmed: 29556109
Angle JC, Morin TH, Solden LM, Narrowe AB, Smith GJ, Borton MA, et al. Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions. Nat Commun. 2017;8:1567. https://doi.org/10.1038/s41467-017-01753-4 .
doi: 10.1038/s41467-017-01753-4
pubmed: 29146959
pmcid: 5691036
Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, et al. Structure and function of the global topsoil microbiome. Nature. 2018;560:233–7. https://doi.org/10.1038/s41586-018-0386-6 .
doi: 10.1038/s41586-018-0386-6
pubmed: 30069051
Berkelmann D, Schneider D, Meryandini A, Daniel R. Unravelling the effects of tropical land use conversion on the soil microbiome. Environmental Microbiome. 2020;15:5. https://doi.org/10.1186/s40793-020-0353-3 .
doi: 10.1186/s40793-020-0353-3
pubmed: 33902736
pmcid: 8067294
Black EM, Just CL. The Genomic Potentials of NOB and Comammox Nitrospira in River Sediment Are Impacted by Native Freshwater Mussels. Front Microbiol. 2018;9:2061. https://doi.org/10.3389/fmicb.2018.02061 .
doi: 10.3389/fmicb.2018.02061
pubmed: 30233538
pmcid: 6131200
Cania B, Vestergaard G, Krauss M, Fliessbach A, Schloter M, Schulz S. A long-term field experiment demonstrates the influence of tillage on the bacterial potential to produce soil structure-stabilizing agents such as exopolysaccharides and lipopolysaccharides. Environmental Microbiome. 2019;14:1. https://doi.org/10.1186/s40793-019-0341-7 .
doi: 10.1186/s40793-019-0341-7
pubmed: 33902712
pmcid: 7989815
Cha G, Meinhardt KA, Orellana LH, Hatt JK, Pannu MW, Stahl DA, et al. The influence of alfalfa-switchgrass intercropping on microbial community structure and function. Environ Microbiol. 2021;23:6828–43. https://doi.org/10.1111/1462-2920.15785 .
doi: 10.1111/1462-2920.15785
pubmed: 34554631
Chen Y-P, Liaw L-L, Kuo J-T, Wu H-T, Wang G-H, Chen X-Q, et al. Evaluation of synthetic gene encoding α-galactosidase through metagenomic sequencing of paddy soil. J Biosci Bioeng. 2019;128:274–82. https://doi.org/10.1016/j.jbiosc.2019.03.006 .
doi: 10.1016/j.jbiosc.2019.03.006
pubmed: 30962101
Chu BTT, Petrovich ML, Chaudhary A, Wright D, Murphy B, Wells G, et al. Metagenomics Reveals the Impact of Wastewater Treatment Plants on the Dispersal of Microorganisms and Genes in Aquatic Sediments. Appl Environ Microbiol. 2018;84 https://doi.org/10.1128/AEM.02168-17 .
Crits-Christoph A, Diamond S, Butterfield CN, Thomas BC, Banfield JF. Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis. Nature. 2018;558:440–4. https://doi.org/10.1038/s41586-018-0207-y .
doi: 10.1038/s41586-018-0207-y
pubmed: 29899444
Hartman WH, Ye R, Horwath WR, Tringe SG. A genomic perspective on stoichiometric regulation of soil carbon cycling. The ISME Journal. 2017;11:2652–65. https://doi.org/10.1038/ismej.2017.115 .
doi: 10.1038/ismej.2017.115
pubmed: 28731470
pmcid: 5702722
Huber DH, Ugwuanyi IR, Malkaram SA, Montenegro-Garcia NA, Lhilhi Noundou V, Chavarria-Palma JE. Metagenome Sequences of Sediment from a Recovering Industrialized Appalachian River in West Virginia. Genome Announcements. 2018;6:e00350–18. https://doi.org/10.1128/genomeA.00350-18 .
doi: 10.1128/genomeA.00350-18
pubmed: 29724837
pmcid: 5940941
Jiang H, Zhou R, Zhang M, Cheng Z, Li J, Zhang G, et al. Exploring the differences of antibiotic resistance genes profiles between river surface water and sediments using metagenomic approach. Ecotoxicol Environ Saf. 2018;161:64–9. https://doi.org/10.1016/j.ecoenv.2018.05.044 .
doi: 10.1016/j.ecoenv.2018.05.044
pubmed: 29859409
Johnston ER, Rodriguez-R LM, Luo C, Yuan MM, Wu L, He Z, et al. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem. Front Microbiol. 2016;7:579. https://doi.org/10.3389/fmicb.2016.00579 .
doi: 10.3389/fmicb.2016.00579
pubmed: 27199914
pmcid: 4842900
Li H-Y, Wang H, Wang H-T, Xin P-Y, Xu X-H, Ma Y, et al. The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales. Microbiome. 2018;6:187. https://doi.org/10.1186/s40168-018-0561-x .
doi: 10.1186/s40168-018-0561-x
pubmed: 30340631
pmcid: 6195703
Li Y, Tremblay J, Bainard LD, Cade-Menun B, Hamel C. Long-term effects of nitrogen and phosphorus fertilization on soil microbial community structure and function under continuous wheat production. Environ Microbiol. 2020;22:1066–88. https://doi.org/10.1111/1462-2920.14824 .
doi: 10.1111/1462-2920.14824
pubmed: 31600863
Links MG, Dumonceaux TJ, McCarthy EL, Hemmingsen SM, Topp E, Town JR. CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems. Microorganisms. 2021;9:816. https://doi.org/10.3390/microorganisms9040816 .
doi: 10.3390/microorganisms9040816
pubmed: 33924343
pmcid: 8069376
Liu Y-R, Johs A, Bi L, Lu X, Hu H-W, Sun D, et al. Unraveling Microbial Communities Associated with Methylmercury Production in Paddy Soils. Environ Sci Technol. 2018;52:13110–8. https://doi.org/10.1021/acs.est.8b03052 .
doi: 10.1021/acs.est.8b03052
pubmed: 30335986
Ma B, Zhao K, Lv X, Su W, Dai Z, Gilbert JA, et al. Genetic correlation network prediction of forest soil microbial functional organization. The ISME Journal. 2018;12:2492–505. https://doi.org/10.1038/s41396-018-0232-8 .
doi: 10.1038/s41396-018-0232-8
pubmed: 30046166
pmcid: 6155114
Neal AL, Hughes D, Clark IM, Jansson JK, Hirsch PR. Microbiome Aggregated Traits and Assembly Are More Sensitive to Soil Management than Diversity. mSystems. 2021;6 https://doi.org/10.1128/mSystems.01056-20 .
Nelkner J, Henke C, Lin TW, Pätzold W, Hassa J, Jaenicke S, et al. Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes. Genes. 2019;10:424. https://doi.org/10.3390/genes10060424 .
doi: 10.3390/genes10060424
pubmed: 31163637
pmcid: 6627896
Orellana LH, Chee-Sanford JC, Sanford RA, Löffler FE, Konstantinidis KT. Year-Round Shotgun Metagenomes Reveal Stable Microbial Communities in Agricultural Soils and Novel Ammonia Oxidizers Responding to Fertilization. Appl Environ Microbiol. 2018;84 https://doi.org/10.1128/AEM.01646-17 .
Ouyang Y, Norton JM. Short-Term Nitrogen Fertilization Affects Microbial Community Composition and Nitrogen Mineralization Functions in an Agricultural Soil. Appl Environ Microbiol. 2020;86:516–8. https://doi.org/10.1128/AEM.02278-19 .
doi: 10.1128/AEM.02278-19
Paungfoo-Lonhienne C, Wang W, Yeoh YK, Halpin N. Legume crop rotation suppressed nitrifying microbial community in a sugarcane cropping soil. Sci Rep. 2017;7:16707. https://doi.org/10.1038/s41598-017-17080-z .
doi: 10.1038/s41598-017-17080-z
pubmed: 29196695
pmcid: 5711877
Romanowicz KJ, Crump BC, Kling GW. Rainfall Alters Permafrost Soil Redox Conditions, but Meta-Omics Show Divergent Microbial Community Responses by Tundra Type in the Arctic. Soil Systems. 2021;5:17. https://doi.org/10.3390/soilsystems5010017 .
doi: 10.3390/soilsystems5010017
Sukhum KV, Vargas RC, Boolchandani M, D’Souza AW, Patel S, Kesaraju A, et al. Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil. mBio. 2021;12 https://doi.org/10.1128/mBio.00798-21 .
Suttner B, Johnston ER, Orellana LH, Rodriguez-R LM, Hatt JK, Carychao D, et al. Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations. Appl Environ Microbiol. 2020;86 https://doi.org/10.1128/AEM.02525-19 .
Wang J, Long Z, Min W, Hou Z. Metagenomic analysis reveals the effects of cotton straw–derived biochar on soil nitrogen transformation in drip-irrigated cotton field. Environ Sci Pollut Res. 2020;27:43929–41. https://doi.org/10.1007/s11356-020-10267-4 .
doi: 10.1007/s11356-020-10267-4
Woodcroft BJ, Singleton CM, Boyd JA, Evans PN, Emerson JB, Zayed AAF, et al. Genome-centric view of carbon processing in thawing permafrost. Nature. 2018;560:49–54. https://doi.org/10.1038/s41586-018-0338-1 .
doi: 10.1038/s41586-018-0338-1
pubmed: 30013118
Wu D, Zhao Y, Cheng L, Zhou Z, Wu Q, Wang Q, et al. Activity and structure of methanogenic microbial communities in sediments of cascade hydropower reservoirs, Southwest China. Sci Total Environ. 2021;786:147515. https://doi.org/10.1016/j.scitotenv.2021.147515 .
doi: 10.1016/j.scitotenv.2021.147515
pubmed: 33975103
Xiao K-Q, Li B, Ma L, Bao P, Zhou X, Zhang T, et al. Metagenomic profiles of antibiotic resistance genes in paddy soils from South China. FEMS Microbiol Ecol. 2016;92:fiw023. https://doi.org/10.1093/femsec/fiw023 .
doi: 10.1093/femsec/fiw023
pubmed: 26850156
Xue Y, Jonassen I, Øvreås L, Taş N. Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost. Microbiology Resource Announcements. 2019;8 https://doi.org/10.1128/MRA.00516-19 .
Yu J, Deem LM, Crow SE, Deenik J, Penton CR. Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential after 2 Years of Biochar Amendment in a Tropical Oxisol. Appl Environ Microbiol. 2019;85 https://doi.org/10.1128/AEM.02957-18 .
Yurgel SN, Nearing JT, Douglas GM, Langille MGI. Metagenomic Functional Shifts to Plant Induced Environmental Changes. Front Microbiol. 2019;10:1682. https://doi.org/10.3389/fmicb.2019.01682 .
doi: 10.3389/fmicb.2019.01682
pubmed: 31404278
pmcid: 6676915
Zhang C, Song Z, Zhuang D, Wang J, Xie S, Liu G. Urea fertilization decreases soil bacterial diversity, but improves microbial biomass, respiration, and N-cycling potential in a semiarid grassland. Biol Fertil Soils. 2019;55:229–42. https://doi.org/10.1007/s00374-019-01344-z .
doi: 10.1007/s00374-019-01344-z
Zheng Z, Li L, Makhalanyane TP, Xu C, Li K, Xue K, et al. The composition of antibiotic resistance genes is not affected by grazing but is determined by microorganisms in grassland soils. Sci Total Environ. 2021;761:143205. https://doi.org/10.1016/j.scitotenv.2020.143205 .
doi: 10.1016/j.scitotenv.2020.143205
pubmed: 33187698
Courtot M, Gupta D, Liyanage I, Xu F, Burdett T. BioSamples database: FAIRer samples metadata to accelerate research data management. Nucleic Acids Res. 2022;50:D1500–7. https://doi.org/10.1093/nar/gkab1046 .
doi: 10.1093/nar/gkab1046
pubmed: 34747489
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1. https://doi.org/10.1093/bioinformatics/btq461 .
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3. https://doi.org/10.1038/nmeth.3869 .
doi: 10.1038/nmeth.3869
pubmed: 27214047
pmcid: 4927377
Shen W, Le S, Li Y, Hu F. SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS One. 2016;11:e0163962. https://doi.org/10.1371/journal.pone.0163962 .
doi: 10.1371/journal.pone.0163962
pubmed: 27706213
pmcid: 5051824
R Core Team, 2021. R: A Language and Environment for Statistical Computing.
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecology Package; 2020.