Sustained bacterial N

Bolan, N. S. & Hedley, M. J. in Handbook of soil acidity 43-70 (CRC Press, 2003).

Rascio, N. & La Rocca, N. in Encyclopedia of Ecology (eds S E Jørgensen & Brian D. F) 412-419 (Academic Press, 2008).

Erisman, J. W., Sutton, M. A., Galloway, J., Klimont, Z. & Winiwarter, W. How a century of ammonia synthesis changed the world. Nature Geosci 1, 636–639 (2008).

doi: 10.1038/ngeo325

IPCC. Climate Change 2022: Mitigation of Climate Change. Working Group III Contribution to the IPCC Sixth Assessment Report. (2022).

Ravishankara, A. R., Daniel, J. S. & Portmann, R. W. Nitrous oxide (N

pubmed: 19713491 doi: 10.1126/science.1176985

Yin, Y. et al. Nitrous oxide is a potent inhibitor of bacterial reductive dechlorination. Environ. Sci. Technol. 53, 692–701 (2019).

pubmed: 30558413 pmcid: 6944068 doi: 10.1021/acs.est.8b05871

Zhang, L. et al. Inhibition of methylmercury and methane formation by nitrous oxide in Arctic tundra soil microcosms. Environ. Sci. Technol. 57, 5655–5665 (2023).

pubmed: 36976621 pmcid: 10100821 doi: 10.1021/acs.est.2c09457

Yin, Y. et al. Nitrous oxide inhibition of methanogenesis represents an underappreciated greenhouse gas emission feedback. ISME J ume 18, wrae027 (2024).

doi: 10.1093/ismejo/wrae027

Braker, G. & Conrad, R. in Advances in Applied Microbiology Vol. 75 (eds Allen I. Laskin, Sima Sariaslani, & Geoffrey M. G) 33-70 (Academic Press, 2011).

Zhou, Y. et al. Nitrous oxide-sink capability of denitrifying bacteria impacted by nitrite and pH. Chem. Eng. J. 428, 132402 (2022).

doi: 10.1016/j.cej.2021.132402

Bristow, L. A. et al. N

doi: 10.1038/ngeo2847

Gao, Y. et al. Competition for electrons favours N

pubmed: 33463871 doi: 10.1111/1462-2920.15404

Senbayram, M. et al. Soil NO

doi: 10.1016/j.soilbio.2019.02.009

Wang, Z., Vishwanathan, N., Kowaliczko, S. & Ishii, S. Clarifying microbial nitrous oxide reduction under aerobic conditions: Tolerant, intolerant, and sensitive. Microbiol. Spectr. 11, e0470922 (2023).

pubmed: 36926990 doi: 10.1128/spectrum.04709-22

Morley, N. & Baggs, E. M. Carbon and oxygen controls on N

doi: 10.1016/j.soilbio.2010.07.008

Sullivan, M. J., Gates, A. J., Appia-Ayme, C., Rowley, G. & Richardson, D. J. Copper control of bacterial nitrous oxide emission and its impact on vitamin B

pubmed: 24248380 pmcid: 3856849 doi: 10.1073/pnas.1314529110

Shen, W. et al. Effects of copper on nitrous oxide (N

doi: 10.1007/s00374-019-01399-y

Blum, J.-M. et al. The pH dependency of N-converting enzymatic processes, pathways and microbes: effect on net N

pubmed: 29411510 doi: 10.1111/1462-2920.14063

Russenes, A. L., Korsaeth, A., Bakken, L. R. & Dörsch, P. Spatial variation in soil pH controls off-season N

doi: 10.1016/j.soilbio.2016.04.019

Buessecker, S. et al. Coupled abiotic-biotic cycling of nitrous oxide in tropical peatlands. Nat. Ecol. Evol. 6, 1–10 (2022).

Breider, F. et al. Response of N

doi: 10.1038/s41558-019-0605-7

Mørkved, P. T., Dörsch, P. & Bakken, L. R. The N

doi: 10.1016/j.soilbio.2007.03.006

Weslien, P., Kasimir Klemedtsson, Å., Börjesson, G. & Klemedtsson, L. Strong pH influence on N

doi: 10.1111/j.1365-2389.2009.01123.x

Palmer, K., Biasi, C. & Horn, M. A. Contrasting denitrifier communities relate to contrasting N

pubmed: 22134649 doi: 10.1038/ismej.2011.172

Lim, N. Y. N., Frostegård, Å. & Bakken, L. R. Nitrite kinetics during anoxia: The role of abiotic reactions versus microbial reduction. Soil Biology and Biochemistry 119, 203–209 (2018).

doi: 10.1016/j.soilbio.2018.01.006

Yang, Y. et al. Organohalide respiration with chlorinated ethenes under low pH conditions. Environ. Sci. Technol. 51, 8579–8588 (2017).

pubmed: 28665587 doi: 10.1021/acs.est.7b01510

Jonassen, K. R. et al. A dual enrichment strategy provides soil-and digestate-competent nitrous oxide-respiring bacteria for mitigating climate forcing in agriculture. mBio 13, e00788–00722 (2022).

pubmed: 35638872 pmcid: 9239227 doi: 10.1128/mbio.00788-22

Van Den Heuvel, R. N., Van Der Biezen, E., Jetten, M. S. M., Hefting, M. M. & Kartal, B. Denitrification at pH 4 by a soil-derived Rhodanobacter-dominated community. Environ. Microbiol. 12, 3264–3271 (2010).

pubmed: 20649643 doi: 10.1111/j.1462-2920.2010.02301.x

Thomsen, J. K., Geest, T. & Cox, R. P. Mass spectrometric studies of the effect of pH on the accumulation of intermediates in denitrification by Paracoccus denitrificans. Appl. Environ. Microbiol. 60, 536–541 (1994).

pubmed: 16349183 pmcid: 201345 doi: 10.1128/aem.60.2.536-541.1994

Bergaust, L., Mao, Y., Bakken Lars, R. & Frostegård, Å. Denitrification response patterns during the transition to anoxic respiration and posttranscriptional effects of suboptimal pH on nitrogen oxide reductase in Paracoccus denitrificans. Appl. Environ. Microbiol 76, 6387–6396 (2010).

pubmed: 20709842 pmcid: 2950438 doi: 10.1128/AEM.00608-10

Olaya-Abril, A. et al. Effect of pH on the denitrification proteome of the soil bacterium Paracoccus denitrificans PD1222. Sci. Rep. 11, 17276 (2021).

pubmed: 34446760 pmcid: 8390676 doi: 10.1038/s41598-021-96559-2

Liu, B., Frostegård, Å. & Bakken, L. R. Impaired reduction of N

doi: 10.1128/mBio.01383-14

Carreira, C., Nunes, R. F., Mestre, O., Moura, I. & Pauleta, S. R. The effect of pH on Marinobacter hydrocarbonoclasticus denitrification pathway and nitrous oxide reductase. J. Biol. Inorg. Chem. 25, 927–940 (2020).

pubmed: 32851479 doi: 10.1007/s00775-020-01812-0

Inubushi, K., Furukawa, Y., Hadi, A., Purnomo, E. & Tsuruta, H. Seasonal changes of CO

pubmed: 12738298 doi: 10.1016/S0045-6535(03)00242-X

Butterbach-Bahl, K., Breuer, L., Gasche, R., Willibald, G. & Papen, H. Exchange of trace gases between soils and the atmosphere in Scots pine forest ecosystems of the northeastern German lowlands: 1. Fluxes of N

doi: 10.1016/S0378-1127(01)00725-3

Karthikeyan, S. et al. Metagenomic characterization of soil microbial communities in the Luquillo experimental forest (Puerto Rico) and implications for nitrogen cycling. Appl. Environ. Microbiol. 87, AEM.00546–00521 (2021).

Sun, Y. et al. pH selects for distinct N

Bueno, E. et al. Anoxic growth of Ensifer meliloti 1021 by N

pubmed: 26074913 pmcid: 4443521 doi: 10.3389/fmicb.2015.00537

Rodriguez-R, L. M. & Konstantinidis, K. T. Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets. Bioinformatics 30, 629–635 (2013).

pubmed: 24123672 doi: 10.1093/bioinformatics/btt584

Sanford, R. A. et al. Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils. Proc. Natl. Acad. Sci. U.S.A. 109, 19709–19714 (2012).

pubmed: 23150571 pmcid: 3511753 doi: 10.1073/pnas.1211238109

Yoon, S., Nissen, S., Park, D., Sanford, R. A. & Löffler, F. E. Nitrous oxide reduction kinetics distinguish bacteria harboring clade I NosZ from those harboring clade II NosZ. Appl. Environ. Microbiol. 82, 3793–3800 (2016).

pubmed: 27084012 pmcid: 4907195 doi: 10.1128/AEM.00409-16

Sánchez-Andrea, I., Stams, A. J. M., Hedrich, S., Ňancucheo, I. & Johnson, D. B. Desulfosporosinus acididurans sp. nov.: an acidophilic sulfate-reducing bacterium isolated from acidic sediments. Extremophiles 19, 39–47 (2015).

pubmed: 25370366 doi: 10.1007/s00792-014-0701-6

Fukushi, M. et al. Biogeochemical implications of N

pubmed: 32866828 pmcid: 7476070 doi: 10.1016/j.isci.2020.101462

Kristoficova, I., Vilhena, C., Behr, S. & Jung, K. BtsT, a novel and specific pyruvate/H

pubmed: 29061664 doi: 10.1128/JB.00599-17

Aramaki, T. et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36, 2251–2252 (2019).

pmcid: 7141845 doi: 10.1093/bioinformatics/btz859

Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28, 45–48 (2000).

pubmed: 10592178 pmcid: 102476 doi: 10.1093/nar/28.1.45

Wang, P.-H. et al. Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates. ISME J 11, 626–640 (2017).

pubmed: 27898054 doi: 10.1038/ismej.2016.158

Frostegård, Å., Vick, S. H. W., Lim, N. Y. N., Bakken, L. R. & Shapleigh, J. P. Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N

doi: 10.1038/s41396-021-01045-2 pubmed: 34489539 pmcid: 8941100

Highton, M. P., Bakken, L. R., Dörsch, P., Molstad, L. & Morales, S. E. Nitrite accumulation and impairment of N

doi: 10.1016/j.soilbio.2021.108529

Alldredge Alice, L. & Cohen, Y. Can microscale chemical patches persist in the sea? Microelectrode study of marine snow, fecal pellets. Science 235, 689–691 (1987).

doi: 10.1126/science.235.4789.689

Loosdrecht, M. C. V., Lyklema, J., Norde, W. & Zehnder, A. J. Influence of interfaces on microbial activity. Microbiol. Rev 54, 75–87 (1990).

pubmed: 2181260 pmcid: 372760 doi: 10.1128/mr.54.1.75-87.1990

Sánchez-Andrea, I., Stams, A. J. M., Amils, R. & Sanz, J. L. Enrichment and isolation of acidophilic sulfate-reducing bacteria from Tinto River sediments. Environ. Microbiol. Rep. 5, 672–678 (2013).

pubmed: 24115617 doi: 10.1111/1758-2229.12066

Lycus, P. et al. Phenotypic and genotypic richness of denitrifiers revealed by a novel isolation strategy. ISME J 11, 2219–2232 (2017).

pubmed: 28696424 pmcid: 5607364 doi: 10.1038/ismej.2017.82

Hausmann, B. et al. Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms. ISME J 10, 2365–2375 (2016).

pubmed: 27015005 pmcid: 4930147 doi: 10.1038/ismej.2016.42

Zhang, L., Wüst, A., Prasser, B., Müller, C. & Einsle, O. Functional assembly of nitrous oxide reductase provides insights into copper site maturation. Proc. Natl. Acad. Sci. 116, 12822–12827 (2019).

pubmed: 31189605 pmcid: 6601269 doi: 10.1073/pnas.1903819116

Simon, J., Einsle, O., Kroneck, P. M. & Zumft, W. G. The unprecedented nos gene cluster of Wolinella succinogenes encodes a novel respiratory electron transfer pathway to cytochrome c nitrous oxide reductase. FEBS Lett 569, 7–12 (2004).

pubmed: 15225600 doi: 10.1016/j.febslet.2004.05.060

Natale, P., Brüser, T. & Driessen, A. J. M. Sec- and Tat-mediated protein secretion across the bacterial cytoplasmic membrane—Distinct translocases and mechanisms. Biochim. Biophys. Acta 1778, 1735–1756 (2008).

pubmed: 17935691 doi: 10.1016/j.bbamem.2007.07.015

Hallin, S., Philippot, L., Löffler, F. E., Sanford, R. A. & Jones, C. M. Genomics and ecology of novel N

pubmed: 28803698 doi: 10.1016/j.tim.2017.07.003

Xianke, C. in Acidophiles (eds Lin J., Chen L., & Lin J.) Ch. 3 (IntechOpen, 2021).

Baker-Austin, C. & Dopson, M. Life in acid: pH homeostasis in acidophiles. Trends Microbiol 15, 165–171 (2007).

pubmed: 17331729 doi: 10.1016/j.tim.2007.02.005

Zengler, K. & Zaramela, L. S. The social network of microorganisms—how auxotrophies shape complex communities. Nat. Rev. Microbiol. 16, 383–390 (2018).

pubmed: 29599459 pmcid: 6059367 doi: 10.1038/s41579-018-0004-5

Embree, M., Liu Joanne, K., Al-Bassam Mahmoud, M. & Zengler, K. Networks of energetic and metabolic interactions define dynamics in microbial communities. Proc. Natl. Acad. Sci. U.S.A. 112, 15450–15455 (2015).

pubmed: 26621749 pmcid: 4687543 doi: 10.1073/pnas.1506034112

Mee, M. T., Collins, J. J., Church, G. M. & Wang, H. H. Syntrophic exchange in synthetic microbial communities. Proc. Natl. Acad. Sci. U.S.A. 111, E2149–E2156 (2014).

pubmed: 24778240 pmcid: 4034247 doi: 10.1073/pnas.1405641111

Jiang, M., Zheng, X. & Chen, Y. Enhancement of denitrification performance with reduction of nitrite accumulation and N

pubmed: 31706124 doi: 10.1016/j.watres.2019.115242

Chang, J. et al. Enhancement of nitrous oxide emissions in soil microbial consortia via copper competition between Proteobacterial methanotrophs and denitrifiers. Appl. Environ. Microbiol. 87, e02301–e02320 (2021).

pubmed: 33355098 pmcid: 8090897 doi: 10.1128/AEM.02301-20

Pan, Y., Ye, L., Ni, B.-J. & Yuan, Z. Effect of pH on N

pubmed: 22749904 doi: 10.1016/j.watres.2012.06.003

Hippe, H. & Stackebrandt, E. in Bergey’s Manual of Systematics of Archaea and Bacteria 1-10 (2015).

Alazard, D., Joseph, M., Battaglia-Brunet, F., Cayol, J.-L. & Ollivier, B. Desulfosporosinus acidiphilus sp. nov.: a moderately acidophilic sulfate-reducing bacterium isolated from acid mining drainage sediments. Extremophiles 14, 305–312 (2010).

pubmed: 20358236 doi: 10.1007/s00792-010-0309-4

Panova, I. A. et al. Desulfosporosinus metallidurans sp. nov., an acidophilic, metal-resistant sulfate-reducing bacterium from acid mine drainage. Int. J. Syst. Evol. Microbiol. 71 (2021). https://doi.org/10.1099/ijsem.0.004876 .

Mardanov, A. V. et al. Genomic insights into a new acidophilic, copper-resistant Desulfosporosinus isolate from the oxidized tailings area of an abandoned gold mine. FEMS Microbiol. Ecol. 92, fiw111 (2016).

pubmed: 27222219 doi: 10.1093/femsec/fiw111

Petzsch, P. et al. Genome sequence of the moderately acidophilic sulfate-reducing Firmicute Desulfosporosinus acididurans (Strain M1

Pester, M. et al. Complete genome sequences of Desulfosporosinus orientis DSM765

pubmed: 23105050 pmcid: 3486391 doi: 10.1128/JB.01392-12

Zhu, K., Ye, X., Ran, H., Zhang, P. & Wang, G. Contrasting effects of straw and biochar on microscale heterogeneity of soil O

doi: 10.1016/j.soilbio.2022.108564

Hiis, E. G. et al. Effective biotechnology for reducing N

Löffler, F. E., Sanford, R. A. & Ritalahti, K. M. in Methods in Enzymology Vol. 397 77-111 (Academic Press, 2005).

Löffler, F. E., Sanford, R. A. & Tiedje, J. M. Initial characterization of a reductive dehalogenase from Desulfitobacterium chlororespirans Co23. Appl. Environ. Microbiol. 62, 3809–3813 (1996).

pubmed: 16535425 pmcid: 1388963 doi: 10.1128/aem.62.10.3809-3813.1996

Chen, G. et al. Anaerobic microbial metabolism of dichloroacetate. mBio 12, e00537–00521 (2021).

pubmed: 33906923 pmcid: 8092247 doi: 10.1128/mBio.00537-21

Klindworth, A. et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41, e1–e1 (2012).

pubmed: 22933715 pmcid: 3592464 doi: 10.1093/nar/gks808

Di Tommaso, P. et al. Nextflow enables reproducible computational workflows. Nat. Biotechnol. 35, 316–319 (2017).

pubmed: 28398311 doi: 10.1038/nbt.3820

Kurtzer, G. M., Sochat, V. & Bauer, M. W. Singularity: Scientific containers for mobility of compute. PLOS ONE 12, e0177459 (2017).

pubmed: 28494014 pmcid: 5426675 doi: 10.1371/journal.pone.0177459

Andrews, S. FastQC: a quality control tool for high throughput sequence data. (2010). https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ .

Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17, 3 (2011).

doi: 10.14806/ej.17.1.200

Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13, 581–583 (2016).

pubmed: 27214047 pmcid: 4927377 doi: 10.1038/nmeth.3869

Seemann, T. barrnap 0.9: rapid ribosomal RNA prediction. (2013). https://github.com/tseemann/barrnap .

Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41, D590–D596 (2012).

pubmed: 23193283 pmcid: 3531112 doi: 10.1093/nar/gks1219

Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).

pubmed: 31341288 pmcid: 7015180 doi: 10.1038/s41587-019-0209-9

Chen, Y. et al. Parallel-Meta Suite: Interactive and rapid microbiome data analysis on multiple platforms. iMeta 1, e1 (2022).

doi: 10.1002/imt2.1

Löffler, F. E., Sun, Q., Li, J. & Tiedje, J. M. 16S rRNA gene-based detection of tetrachloroethene-dechlorinating Desulfuromonas and Dehalococcoides species. Appl. Environ. Microbiol. 66, 1369–1374 (2000).

pubmed: 10742213 pmcid: 91994 doi: 10.1128/AEM.66.4.1369-1374.2000

Ye, J. et al. Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13, 134 (2012).

pubmed: 22708584 pmcid: 3412702 doi: 10.1186/1471-2105-13-134

Ritalahti, K. M. et al. Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains. Appl. Environ. Microbiol. 72, 2765–2774 (2006).

pubmed: 16597981 pmcid: 1449079 doi: 10.1128/AEM.72.4.2765-2774.2006

Krakau, S., Straub, D., Gourlé, H., Gabernet, G. & Nahnsen, S. nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning. NAR Genom. Bioinform. 4, lqac007 (2022).

pubmed: 35118380 pmcid: 8808542 doi: 10.1093/nargab/lqac007

Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).

pubmed: 30423086 pmcid: 6129281 doi: 10.1093/bioinformatics/bty560

Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

pubmed: 22388286 pmcid: 3322381 doi: 10.1038/nmeth.1923

Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015).

pubmed: 25609793 doi: 10.1093/bioinformatics/btv033

Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).

pubmed: 31388474 pmcid: 6662567 doi: 10.7717/peerj.7359

Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25, 1043–1055 (2015).

pubmed: 25977477 pmcid: 4484387 doi: 10.1101/gr.186072.114

Gemayel, K., Lomsadze, A. & Borodovsky, M. MetaGeneMark-2: Improved Gene Prediction in Metagenomes. bioRxiv, 2022.2007.2025.500264 (2022). https://doi.org/10.1101/2022.07.25.500264 .

Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).

pubmed: 20003500 pmcid: 2803857 doi: 10.1186/1471-2105-10-421

Overbeek, R. et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42, D206–D214 (2013).

pubmed: 24293654 pmcid: 3965101 doi: 10.1093/nar/gkt1226

Rodriguez-R, L. M. & Konstantinidis, K. T. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ https://doi.org/10.7287/peerj.preprints.1900v1 (2016).

Hallgren, J. et al. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. bioRxiv, 2022.2004.2008.487609 (2022). https://doi.org/10.1101/2022.04.08.487609 .

Gilchrist, C. L. M. et al. cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters. Bioinformatics Advances 1, vbab016 (2021).

pubmed: 36700093 pmcid: 9710679 doi: 10.1093/bioadv/vbab016

Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925–1927 (2019).

pubmed: 31730192 pmcid: 7703759 doi: 10.1093/bioinformatics/btz848

Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35, 4453–4455 (2019).

pubmed: 31070718 pmcid: 6821337 doi: 10.1093/bioinformatics/btz305

Darriba, D. et al. ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Mol. Biol. Evol. 37, 291–294 (2019).

pmcid: 6984357 doi: 10.1093/molbev/msz189

Kim, D., Park, S. & Chun, J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J. Microbiol. 59, 476–480 (2021).

pubmed: 33907973 doi: 10.1007/s12275-021-1154-0

Yu, G., Smith, D. K., Zhu, H., Guan, Y. & Lam, T. T.- Y. ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol. Evol. 8, 28–36 (2017).

doi: 10.1111/2041-210X.12628

Orellana, L. H., Rodriguez-R, L. M. & Konstantinidis, K. T. ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores. Nucleic Acids Res 45, e14–e14 (2016).

pmcid: 5388429

Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

pubmed: 23329690 pmcid: 3603318 doi: 10.1093/molbev/mst010

Dearth, S. P. et al. Metabolome changes are induced in the arbuscular mycorrhizal fungus Gigaspora margarita by germination and by its bacterial endosymbiont. Mycorrhiza 28, 421–433 (2018).

pubmed: 29860608 doi: 10.1007/s00572-018-0838-8

Lu, W. et al. Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer. Anal. Chem. 82, 3212–3221 (2010).

pubmed: 20349993 pmcid: 2863137 doi: 10.1021/ac902837x

Clasquin, M. F., Melamud, E. & Rabinowitz, J. D. LC-MS data processing with MAVEN: A metabolomic analysis and visualization engine. Curr. Protoc. Bioinformatics 37, 14.11.11–14.11.23 (2012).

doi: 10.1002/0471250953.bi1411s37

Sander, R. Compilation of Henry’s law constants (version 4.0) for water as solvent. Atmos. Chem. Phys. 15, 4399–4981 (2015).

doi: 10.5194/acp-15-4399-2015

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Guang He (G)

Gao Chen (G)

Yongchao Xie (Y)

Cynthia M Swift (CM)

Diana Ramirez (D)

Gyuhyon Cha (G)

Konstantinos T Konstantinidis (KT)

Mark Radosevich (M)

Frank E Löffler (FE)

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