Investigating plant-microbe interactions within the root.
Genetic manipulation
Microbe–microbe interactions
Omics
Plant–microbe interactions
Root microbiome
Journal
Archives of microbiology
ISSN: 1432-072X
Titre abrégé: Arch Microbiol
Pays: Germany
ID NLM: 0410427
Informations de publication
Date de publication:
22 Sep 2022
22 Sep 2022
Historique:
received:
13
05
2022
accepted:
12
09
2022
revised:
15
07
2022
entrez:
22
9
2022
pubmed:
23
9
2022
medline:
28
9
2022
Statut:
epublish
Résumé
A diverse lineage of microorganisms inhabits plant roots and interacts with plants in various ways. Further, these microbes communicate and interact with each other within the root microbial community. These symbioses add an array of influences, such as plant growth promotion or indirect protection to the host plant. Omics technology and genetic manipulation have been applied to unravel these interactions. Recent studies probed plants' control over microbes. However, the activity of the root microbial community under host influence has not been elucidated enough. In this mini-review, we discussed the recent advances and limits of omics technology and genetics for dissecting the activity of the root-associated microbial community. These materials may help us formulate the correct experimental plans to capture the entire molecular mechanisms of the plant-microbe interaction.
Identifiants
pubmed: 36136275
doi: 10.1007/s00203-022-03257-2
pii: 10.1007/s00203-022-03257-2
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
639Subventions
Organisme : Japan Society for the Promotion of Science
ID : 20H02986
Organisme : Japan Society for the Promotion of Science
ID : 20H02986
Organisme : Japan Science and Technology Agency
ID : JPMJFR200A
Organisme : Japan Science and Technology Agency
ID : JPMJFR200A
Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Références
Agler MT, Ruhe J, Kroll S, Morhenn C, Kim ST, Weigel D, Kemen EM (2016) Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLoS Biol 14:e1002352. https://doi.org/10.1371/journal.pbio.1002352
doi: 10.1371/journal.pbio.1002352
pubmed: 26788878
pmcid: 4720289
Álvarez C, Brenes-Álvarez M, Molina-Heredia FP, Mariscal V (2022) Quantitative proteomics at early stages of the symbiotic interaction between Oryza sativa and Nostoc punctiforme reveals novel proteins involved in the symbiotic crosstalk. Plant Cell Physiol. https://doi.org/10.1093/PCP/PCAC043
doi: 10.1093/PCP/PCAC043
pubmed: 35373828
Amann R, Snaidr J, Wagner M, Ludwig W, Schleifer KH (1996) In situ visualization of high genetic diversity in a natural microbial community. J Bacteriol 178:3496–3500. https://doi.org/10.1128/JB.178.12.3496-3500.1996
doi: 10.1128/JB.178.12.3496-3500.1996
pubmed: 8655546
pmcid: 178118
Andrés-Barrao C, Alzubaidy H, Jalal R, Mariappan KG, de Zélicourt A, Bokhari A, Artyukh O, Alwutayd K, Rawat A, Shekhawat K, Almeida-Trapp M, Saad MM, Hirt H (2021) Coordinated bacterial and plant sulfur metabolism in Enterobacter sp. SA187-induced plant salt stress tolerance. Proc Natl Acad Sci USA 118:e2107417118. https://doi.org/10.1073/PNAS.2107417118
doi: 10.1073/PNAS.2107417118
pubmed: 34772809
pmcid: 8609655
Angulo V, Beriot N, Garcia-Hernandez E, Li E, Masteling R, Lau JA (2022) Plant–microbe eco-evolutionary dynamics in a changing world. New Phytol 234:1919–1928. https://doi.org/10.1111/NPH.18015
doi: 10.1111/NPH.18015
pubmed: 35114015
Babenko LM, Kosakivska IV, Romanenko КO (2021) Molecular mechanisms of N-acyl homoserine lactone signals perception by plants. Cell Biol Int 46:523–534. https://doi.org/10.1002/CBIN.11749
doi: 10.1002/CBIN.11749
pubmed: 34937124
Bai Y, Müller DB, Srinivas G, Garrido-Oter R, Potthoff E, Rott M, Dombrowski N, Münch PC, Spaepen S, Remus-Emsermann M, Hüttel B, McHardy AC, Vorholt JA, Schulze-Lefert P (2015) Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528:364–369. https://doi.org/10.1038/nature16192
doi: 10.1038/nature16192
pubmed: 26633631
Barlow JT, Bogatyrev SR, Ismagilov RF (2020) A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities. Nat Commun 11:2590. https://doi.org/10.1038/s41467-020-16224-6
doi: 10.1038/s41467-020-16224-6
pubmed: 32444602
pmcid: 7244552
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J et al (2019) Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37:852–857. https://doi.org/10.1038/S41587-019-0209-9
doi: 10.1038/S41587-019-0209-9
pubmed: 31341288
pmcid: 7015180
Brader G, Compant S, Vescio K, Mitter B, Trognitz F, Ma LJ, Sessitsch A (2017) Ecology and genomic insights into plant-pathogenic and plant-nonpathogenic endophytes. Ann Rev Phytopathol 55:61–83. https://doi.org/10.1146/annurev-phyto-080516-035641
doi: 10.1146/annurev-phyto-080516-035641
Broberg M, Doonan J, Mundt F, Denman S, McDonald JE (2018) Integrated multi-omic analysis of host-microbiota interactions in acute oak decline. Microbiome 6:21. https://doi.org/10.1186/S40168-018-0408-5
doi: 10.1186/S40168-018-0408-5
pubmed: 29378627
pmcid: 5789699
Bulgarelli D, Rott M, Schlaeppi K, Loren V, van Themaat E, Ahmadinejad N, Assenza F, Rauf P, Huettel B, Reinhardt R, Schmelzer E, Peplies J, Gloeckner FO, Amann R, Eickhorst T, Schulze-Lefert P (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488:91–95. https://doi.org/10.1038/nature11336
doi: 10.1038/nature11336
pubmed: 22859207
Burke C, Steinberg P, Rusch D, Kjelleberg S, Thomas T (2011) Bacterial community assembly based on functional genes rather than species. Proc Natl Acad Sci USA 108:14288–14293. https://doi.org/10.1073/pnas.1101591108
doi: 10.1073/pnas.1101591108
pubmed: 21825123
pmcid: 3161577
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. https://doi.org/10.1038/nmeth.f.303
doi: 10.1038/nmeth.f.303
pubmed: 20383131
pmcid: 3156573
Chase JM (2007) Drought mediates the importance of stochastic community assembly. Proc Natl Acad Sci USA 104:17430–17434. https://doi.org/10.1073/pnas.0704350104
doi: 10.1073/pnas.0704350104
pubmed: 17942690
pmcid: 2077273
Choi V, Jeong S, Kim E (2022) Variation of the seed endophytic bacteria among plant populations and their plant growth-promoting activities in a wild mustard plant species, Capsella bursa- pastoris. Ecol Evol 12:e8683. https://doi.org/10.1002/ece3.8683
doi: 10.1002/ece3.8683
pubmed: 35309752
pmcid: 8901890
Delmotte N, Ahrens CH, Knief C, Qeli E, Koch M, Fischer HM, Vorholt JA, Hennecke H, Pessi G (2010) An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules. Proteomics 10:1391–1400. https://doi.org/10.1002/PMIC.200900710
doi: 10.1002/PMIC.200900710
pubmed: 20104621
Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V (2015) Structure variation and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci U S A 112:E911–E920. https://doi.org/10.1073/pnas.1414592112
doi: 10.1073/pnas.1414592112
Estrela S, Vila JCC, Lu N, Bajić D, Rebolleda-Gómez M, Chang CY, Goldford JE, Sanchez-Gorostiaga A, Sánchez Á (2022) Functional attractors in microbial community assembly. Cell Syst 13:29-42.e7. https://doi.org/10.1016/j.cels.2021.09.011
doi: 10.1016/j.cels.2021.09.011
pubmed: 34653368
Finkel OM, Delmont TO, Post AF, Belkin S (2016) Metagenomic signatures of bacterial adaptation to life in the phyllosphere of a salt-secreting desert tree. Appl Environ Microbiol 82:2854–2861. https://doi.org/10.1128/AEM.00483-16
doi: 10.1128/AEM.00483-16
pubmed: 26944845
pmcid: 4836421
Finkel OM, Salas-González I, Castrillo G, Spaepen S, Law TF, Teixeira PJPL, Jones CD, Dangl JL (2019) The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response. PLoS Biol 17:e3000534. https://doi.org/10.1371/journal.pbio.3000534
doi: 10.1371/journal.pbio.3000534
pubmed: 31721759
pmcid: 6876890
Fitzpatrick CR, Copeland J, Wang PW, Guttman DS, Kotanen PM, Johnson MTJ (2018) Assembly and ecological function of the root microbiome across angiosperm plant species. Proc Natl Acad Sci U S A 115:E1157–E1165. https://doi.org/10.1073/pnas.1717617115
doi: 10.1073/pnas.1717617115
pubmed: 29358405
pmcid: 5819437
Gowda K, Ping D, Mani M, Kuehn S (2022) Genomic structure predicts metabolite dynamics in microbial communities. Cell 185:530-546.e25. https://doi.org/10.1016/J.CELL.2021.12.036
doi: 10.1016/J.CELL.2021.12.036
pubmed: 35085485
Guo CJ, Allen BM, Hiam KJ, Dodd D, Van Treuren W, Higginbottom S, Nagashima K, Fischer CR, Sonnenburg JL, Spitzer MH, Fischbach MA (2019) Depletion of microbiome-derived molecules in the host using Clostridium genetics. Science 366:eaav1282. https://doi.org/10.1126/science.aav1282
Guo X, Zhang X, Qin Y, Liu YX, Zhang J, Zhang N, Wu K, Qu B, He Z, Wang X, Zhang X, Hacquard S, Fu X, Bai Y (2019) Host-associated quantitative abundance profiling reveals the microbial load variation of root microbiome. Plant Commun 1:100003. https://doi.org/10.1016/j.xplc.2019.100003
doi: 10.1016/j.xplc.2019.100003
Hara S, Wada N, Hsiao SS-Y, Zhang M, Bao Z, Iizuka Y, Lee DC, Sato S, Tang SL, Minamisawa K (2022) In vivo evidence of single
doi: 10.1128/MBIO.01255-22
pubmed: 35608299
Harbort CJ, Hashimoto M, Inoue H, Niu Y, Guan R, Rombolà AD, Kopriva S, Voges MJEEE, Sattely ES, Garrido-Oter R, Schulze-Lefert P (2020) Root-secreted coumarins and the microbiota interact to improve iron nutrition in Arabidopsis. Cell Host Microbe 28:825-837.e6. https://doi.org/10.1016/j.chom.2020.09.006
doi: 10.1016/j.chom.2020.09.006
pubmed: 33027611
pmcid: 7738756
Haque A, Engel J, Teichmann SA, Lönnberg T (2017) A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genome Med 9:75. https://doi.org/10.1186/s13073-017-0467-4
doi: 10.1186/s13073-017-0467-4
pubmed: 28821273
pmcid: 5561556
Hiruma K, Gerlach N, Sacristán S, Nakano RT, Hacquard S, Kracher B, Neumann U, Ramírez D, Bucher M, O’Connell RJ, Schulze-Lefert P (2016) Root endophyte Colletotrichum tofieldiae confers plant fitness benefits that are phosphate status dependent. Cell 165:464–474. https://doi.org/10.1016/j.cell.2016.02.028
doi: 10.1016/j.cell.2016.02.028
pubmed: 26997485
pmcid: 4826447
Imdahl F, Vafadarnejad E, Homberger C, Saliba AE, Vogel J (2020) Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria. Nat Microbiol 5:1202–1206. https://doi.org/10.1038/s41564-020-0774-1
doi: 10.1038/s41564-020-0774-1
pubmed: 32807892
Jin WB, Li TT, Huo D, Qu S, Li XV, Arifuzzaman M, Lima SF, Shi HQ, Wang A, Putzel GG, Longman RS, Artis D, Guo CJ (2022) Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome. Cell 185:547-562.e22. https://doi.org/10.1016/J.CELL.2021.12.035
doi: 10.1016/J.CELL.2021.12.035
pubmed: 35051369
Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P, Chen L, Leopold SR, Hanson BM, Agresta HO, Gerstein M, Sodergren E, Weinstock GM (2019) Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun 10:5029. https://doi.org/10.1038/s41467-019-13036-1
doi: 10.1038/s41467-019-13036-1
pubmed: 31695033
pmcid: 6834636
Karasov TL, Almario J, Friedemann C, Ding W, Giolai M, Heavens D, Kersten S, Lundberg DS, Neumann M, Regalado J, Neher RA, Kemen E, Weigel D (2018) Arabidopsis thaliana and Pseudomonas pathogens exhibit stable associations over evolutionary timescales. Cell Host Microbe 24:168-179.e4. https://doi.org/10.1016/J.CHOM.2018.06.011
doi: 10.1016/J.CHOM.2018.06.011
pubmed: 30001519
pmcid: 6054916
Knapp DG, Lázár A, Molnár A, Vajna B, Karácsony Z, Váczy KZ, Kovács GM (2021) Above-ground parts of white grapevine Vitis vinifera cv. furmint share core members of the fungal microbiome. Environ Microbiol Rep 13:509–520. https://doi.org/10.1111/1758-2229.12950
doi: 10.1111/1758-2229.12950
pubmed: 33951321
Knief C, Delmotte N, Chaffron S, Stark M, Innerebner G, Wassmann R, Von Mering C, Vorholt JA (2012) Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J 6:1378–1390. https://doi.org/10.1038/ismej.2011.192
doi: 10.1038/ismej.2011.192
pubmed: 22189496
Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA (2015) The technology and biology of single-cell RNA sequencing. Mol Cell 58:610–620. https://doi.org/10.1016/j.molcel.2015.04.005
doi: 10.1016/j.molcel.2015.04.005
pubmed: 26000846
Lam TJ, Stamboulian M, Han W, Ye Y (2020) Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species. PLoS Comput Biol 16:e1007951. https://doi.org/10.1371/journal.pcbi.1007951
doi: 10.1371/journal.pcbi.1007951
pubmed: 33125363
pmcid: 7657538
Lardi M, Liu Y, Purtschert G, Bolzan de Campos SB, Pessi G (2017) Transcriptome analysis of Paraburkholderia phymatum under nitrogen starvation and during symbiosis with Phaseolus vulgaris. Genes 8:389. https://doi.org/10.3390/GENES8120389
doi: 10.3390/GENES8120389
pmcid: 5748707
Lebeis SL, Paredes SH, Lundberg DS, Breakfield N, Gehring J, McDonald M, Malfatti S, Glavina del Rio TG, Jones CD, Tringe SG, Dangl JL (2015) Plant microbiome. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 349:860–864. https://doi.org/10.1126/science.aaa8764
doi: 10.1126/science.aaa8764
pubmed: 26184915
Louca S, Jacques SMS, Pires APF, Leal JS, Srivastava DS, Parfrey LW, Farjalla VF, Doebeli M (2016) High taxonomic variability despite stable functional structure across microbial communities. Nat Ecol Evol 1:15. https://doi.org/10.1038/s41559-016-0015
doi: 10.1038/s41559-016-0015
pubmed: 28812567
Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, Del Rio TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86–90. https://doi.org/10.1038/nature11237
doi: 10.1038/nature11237
pubmed: 22859206
pmcid: 4074413
Lundberg DS, Pramoj Na Ayutthaya PPN, Strauß A, Shirsekar G, Lo WS, Lahaye T, Weigel D (2021) Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition. Elife. https://doi.org/10.7554/eLife.66186
doi: 10.7554/eLife.66186
pubmed: 34292157
pmcid: 8387020
Lundberg DS, Yourstone S, Mieczkowski P, Jones CD, Dangl JL (2013) Practical innovations for high-throughput amplicon sequencing. Nat Methods 10:999–1002. https://doi.org/10.1038/nmeth.2634
doi: 10.1038/nmeth.2634
pubmed: 23995388
Mahdi LK, Miyauchi S, Uhlmann C, Garrido-Oter R, Langen G, Wawra S, Niu Y, Guan R, Robertson-Albertyn S, Bulgarelli D, Parker JE, Zuccaro A (2022) The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. ISME J 16:876–889. https://doi.org/10.1038/s41396-021-01138-y
doi: 10.1038/s41396-021-01138-y
pubmed: 34686763
Matsumoto A, Schlüter T, Melkonian K, Takeda A, Nakagami H, Mine A (2022) A versatile Tn7 transposon-based bioluminescence tagging tool for quantitative and spatial detection of bacteria in plants. Plant Commun 3:100227. https://doi.org/10.1016/J.XPLC.2021.100227
doi: 10.1016/J.XPLC.2021.100227
pubmed: 35059625
McAllister KN, Bouillaut L, Kahn JN, Self WT, Sorg JA (2017) Using CRISPR-Cas9-mediated genome editing to generate C. difficile mutants defective in selenoproteins synthesis. Sci Rep 7:14672. https://doi.org/10.1038/S41598-017-15236-5
doi: 10.1038/S41598-017-15236-5
pubmed: 29116155
pmcid: 5677094
Mohr W, Lehnen N, Ahmerkamp S, Marchant HK, Graf JS, Tschitschko B, Yilmaz P, Littmann S, Gruber-Vodicka H, Leisch N, Weber M, Lott C, Schubert CJ, Milucka J, Kuypers MMM (2021) Terrestrial-type nitrogen-fixing symbiosis between seagrass and a marine bacterium. Nature 600:105–109. https://doi.org/10.1038/s41586-021-04063-4
doi: 10.1038/s41586-021-04063-4
pubmed: 34732889
pmcid: 8636270
Musat N, Musat F, Weber PK, Pett-Ridge J (2016) Tracking microbial interactions with NanoSIMS. Curr Opin Biotechnol 41:114–121. https://doi.org/10.1016/J.COPBIO.2016.06.007
doi: 10.1016/J.COPBIO.2016.06.007
pubmed: 27419912
Negrel L, Halter D, Wiedemann-Merdinoglu S, Rustenholz C, Merdinoglu D, Hugueney P, Baltenweck R (2018) Identification of lipid markers of Plasmopara viticola infection in grapevine using a non-targeted metabolomic approach. Front Plant Sci 9:360. https://doi.org/10.3389/fpls.2018.00360
doi: 10.3389/fpls.2018.00360
pubmed: 29619037
pmcid: 5871909
Nobori T, Velásquez AC, Wu J, Kvitko BH, Kremer JM, Wang Y, He SY, Tsuda K (2018) Transcriptome landscape of a bacterial pathogen under plant immunity. Proc Natl Acad Sci U S A 115:E3055–E3064. https://doi.org/10.1073/PNAS.1800529115
doi: 10.1073/PNAS.1800529115
pubmed: 29531038
pmcid: 5879711
Nobori T, Wang Y, Wu J, Stolze SC, Tsuda Y, Finkemeier I, Nakagami H, Tsuda K (2020) Multidimensional gene regulatory landscape of a bacterial pathogen in plants. Nat Plants 6:883–896. https://doi.org/10.1038/s41477-020-0690-7
doi: 10.1038/s41477-020-0690-7
pubmed: 32541952
O’Connell RJ, Thon MR, Hacquard S, Amyotte SG, Kleemann J, Torres MF, Damm U, Buiate EA, Epstein L, Alkan N, Altmüller J, Alvarado-Balderrama L, Bauser CA, Becker C, Birren BW, Chen Z, Choi J, Crouch JA, Duvick JP et al (2012) Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nat Genet 44:1060–1065. https://doi.org/10.1038/ng.2372
doi: 10.1038/ng.2372
pubmed: 22885923
Pathak KV, Keharia H (2013) Characterization of fungal antagonistic bacilli isolated from aerial roots of banyan (Ficus benghalensis) using intact-cell MALDI-TOF mass spectrometry (ICMS). J Appl Microbiol 114:1300–1310. https://doi.org/10.1111/JAM.12161
doi: 10.1111/JAM.12161
pubmed: 23387377
Plyuta VA, Chernikova AS, Sidorova DE, Kupriyanova EV, Koksharova OA, Chernin LS, Khmel IA (2021) Modulation of Arabidopsis thaliana growth by volatile substances emitted by Pseudomonas and Serratia strains. World J Microbiol Biotechnol 37:82. https://doi.org/10.1007/S11274-021-03047-W
doi: 10.1007/S11274-021-03047-W
pubmed: 33855623
Regalado J, Lundberg DS, Deusch O, Kersten S, Karasov T, Poersch K, Shirsekar G, Weigel D (2020) Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves. ISME J 14:2116–2130. https://doi.org/10.1038/s41396-020-0665-8
doi: 10.1038/s41396-020-0665-8
pubmed: 32405027
pmcid: 7368051
Rosenberg E, Zilber-Rosenberg I (2018) The hologenome concept of evolution after 10 years. Microbiome 6:78. https://doi.org/10.1186/S40168-018-0457-9
doi: 10.1186/S40168-018-0457-9
pubmed: 29695294
pmcid: 5922317
Rubin BE, Diamond S, Cress BF, Crits-Christoph A, Lou YC, Borges AL, Shivram H, He C, Xu M, Zhou Z, Smith SJ, Rovinsky R, Smock DCJ, Tang K, Owens TK, Krishnappa N, Sachdeva R, Barrangou R, Deutschbauer AM et al (2022) Species- and site-specific genome editing in complex bacterial communities. Nat Microbiol 7:34–47. https://doi.org/10.1038/s41564-021-01014-7
doi: 10.1038/s41564-021-01014-7
pubmed: 34873292
Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA 109:6241–6246. https://doi.org/10.1073/PNAS.1117018109
doi: 10.1073/PNAS.1117018109
Sheng K, Cao W, Niu Y, Deng Q, Zong C (2017) Effective detection of variation in single-cell transcriptomes using MATQ-seq. Nat Methods 14:267–270. https://doi.org/10.1038/nmeth.4145
doi: 10.1038/nmeth.4145
pubmed: 28092691
Slavov N (2020) Unpicking the proteome in single cells. Science 367:512–513. https://doi.org/10.1126/SCIENCE.AAZ6695
doi: 10.1126/SCIENCE.AAZ6695
pubmed: 32001644
pmcid: 7029782
Song L, Xie K (2020) Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing. Microbiome 8:80. https://doi.org/10.1186/S40168-020-00859-0
doi: 10.1186/S40168-020-00859-0
pubmed: 32493511
pmcid: 7268715
Steiger MG (2021) Flow Cytometry for Filamentous Fungi. Methods Mol Biol 2234:147–155. https://doi.org/10.1007/978-1-0716-1048-0_13
doi: 10.1007/978-1-0716-1048-0_13
pubmed: 33165787
Utami YD, Kuwahara H, Murakami T, Morikawa T, Sugaya K, Kihara K, Yuki M, Lo N, Deevong P, Hasin S, Boonriam W, Inoue T, Yamada A, Ohkuma M, Hongoh Y (2018) Phylogenetic diversity and single-cell genome analysis of ‘Melainabacteria’, a non-photosynthetic cyanobacterial group, in the termite gut. Microbes Environ 33:50–57. https://doi.org/10.1264/jsme2.ME17137
doi: 10.1264/jsme2.ME17137
pubmed: 29415909
pmcid: 5877343
Vági P, Knapp DG, Kósa A, Seress D, Horváth ÁN, Kovács GM (2014) Simultaneous specific in planta visualization of root-colonizing fungi using fluorescence in situ hybridization (FISH). Mycorrhiza 24:259–266. https://doi.org/10.1007/S00572-013-0533-8
doi: 10.1007/S00572-013-0533-8
pubmed: 24221902
Velásquez AC, Huguet-Tapia JC, He SY (2022) Shared in planta population and transcriptomic features of nonpathogenic members of endophytic phyllosphere microbiota. Proc Natl Acad Sci U S A 119:e2114460119. https://doi.org/10.1073/PNAS.2114460119
doi: 10.1073/PNAS.2114460119
pubmed: 35344425
pmcid: 9168490
Voges MJEEE, Bai Y, Schulze-Lefert P, Sattely ES (2019) Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome. Proc Natl Acad Sci U S A 116:12558–12565. https://doi.org/10.1073/PNAS.1820691116
doi: 10.1073/PNAS.1820691116
pubmed: 31152139
pmcid: 6589675
Vorholt JA, Vogel C, Carlström CI, Müller DB (2017) Establishing causality: opportunities of synthetic communities for plant microbiome research. Cell Host Microbe 22:142–155. https://doi.org/10.1016/J.CHOM.2017.07.004
doi: 10.1016/J.CHOM.2017.07.004
pubmed: 28799900
Xu L, Naylor D, Dong Z, Simmons T, Pierroz G, Hixson KK, Kim YM, Zink EM, Engbrecht KM, Wang Y, Gao C, DeGraaf S, Madera MA, Sievert JA, Hollingsworth J, Birdseye D, Scheller HV, Hutmacher R, Dahlberg J et al (2018) Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proc Natl Acad Sci U S A 115:E4284–E4293. https://doi.org/10.1073/PNAS.1717308115
doi: 10.1073/PNAS.1717308115
pubmed: 29666229
pmcid: 5939072
Yu P, He X, Baer M, Beirinckx S, Tian T, Moya YAT, Zhang X, Deichmann M, Frey FP, Bresgen V, Li C, Razavi BS, Schaaf G, von Wirén N, Su Z, Bucher M, Tsuda K, Goormachtig S, Chen X, Hochholdinger F (2021) Plant flavones enrich rhizosphere Oxalobacteraceae to improve maize performance under nitrogen deprivation. Nat Plants 7:481–499. https://doi.org/10.1038/s41477-021-00897-y
doi: 10.1038/s41477-021-00897-y
pubmed: 33833418
Yu X, Lund SP, Greenwald JW, Records AH, Scott RA, Nettleton D, Lindow SE, Gross DC, Beattie GA (2014) Transcriptional analysis of the global regulatory networks active in Pseudomonas syringae during leaf colonization. Mbio 5:e01683–e11614. https://doi.org/10.1128/mBio.01683-14
doi: 10.1128/mBio.01683-14
pubmed: 25182327
pmcid: 4173789
Zhang W, Corwin JA, Copeland DH, Feusier J, Eshbaugh R, Cook DE, Atwell S, Kliebenstein DJ (2019) Plant–necrotroph co-transcriptome networks illuminate a metabolic battlefield. Elife 8:e44279. https://doi.org/10.7554/eLife.44279
doi: 10.7554/eLife.44279
pubmed: 31081752
pmcid: 6557632