Abanda-Nkpwatt D, Musch M, Tschiersch J et al. Molecular interaction between
283
Methylobacterium extorquens and seedlings: growth promotion, methanol
284
consumption, and localization of the methanol emission site. J Exp Bot
285
2006;57:4025-32. https://doi.org/10.1093/Jxb/Erl173.
286
Aronson EL, Allison SD, Helliker BR. Environmental impacts on the diversity of
287
methane-cycling microbes and their resultant function. Front Microbiol 2013;4:225.
288
https://doi.org/10.3389/fmicb.2013.00225.
289
Aulakh MS, Wassmann R, Rennenberg H et al. Pattern and amount of aerenchyma
290
relate to variable methane transport capacity of different rice cultivars. Plant Biol
291
2000;2:182-94. https://doi.org/10.1055/s-2000-9161.
292
Bruhn D, Moller IM, Mikkelsen TN et al. Terrestrial plant methane production and
293
emission. Physiol Plant 2012;144:201-9. https://doi.org/10.1111/j.1399-
294
3054.2011.01551.x.
295
296
297
Butenhoff CL, Khalil MAK. Global methane emissions from terrestrial plants. Environ
Sci Technol 2007;41:4032-47. https://doi.org/10.1021/es062404i.
Delmotte N, Knief C, Chaffron S et al. Community proteogenomics reveals insights
298
into the physiology of phyllosphere bacteria. Proc Natl Acad Sci USA
299
2009;106:16428-33. https://doi.org/10.1073/pnas.0905240106.
300
Dourado MN, Camargo Neves AA, Santos DS et al. Biotechnological and agronomic
301
potential of endophytic pink-pigmented methylotrophic Methylobacterium spp.
302
Biomed Res Int 2015;2015:909016. https://doi.org/10.1155/2015/909016.
303
Fall R, Benson AA. Leaf methanol - the simplest natural product from plants. Trends
304
Plant Sci 1996;1:296-301. https://doi.org/10.1016/S1360-1385(96)88175-0.
305
Finkel OM, Burch AY, Lindow SE et al. Geographical location determines the
12
306
population structure in phyllosphere microbial communities of a salt-excreting desert
307
tree. Appl Environ Microbiol 2011;77:7647-55. https://doi.org/10.1128/AEM.05565-
308
11.
309
Galbally IE, Kirstine W. The production of methanol by flowering plants and the global
310
cycle of methanol. J Atmos Chem 2002;43:195-229.
311
https://doi.org/10.1023/A:1020684815474.
312
Gargallo-Garriga A, Sardans J, Perez-Trujillo M et al. Shifts in plant foliar and floral
313
metabolomes in response to the suppression of the associated microbiota. BMC Plant
314
Biol 2016;16:78. https://doi.org/10.1186/s12870-016-0767-7.
315
Gourion B, Francez-Charlot A, Vorholt JA. PhyR is involved in the general stress
316
response of Methylobacterium extorquens AM1. J Bacteriol 2008;190:1027-35.
317
https://doi.org/10.1128/JB.01483-07.
318
Gourion B, Rossignol M, Vorholt JA. A proteomic study of Methylobacterium
319
extorquens reveals a response regulator essential for epiphytic growth. Proc Natl
320
Acad Sci USA 2006;103:13186-91. https://doi.org/10.1073/pnas.0603530103.
321
Gourion B, Sulser S, Frunzke J et al. The PhyR-sEcfG signalling cascade is involved in
322
stress response and symbiotic efficiency in Bradyrhizobium japonicum. Mol
323
Microbiol 2009;73:291-305. https://doi.org/10.1111/j.1365-2958.2009.06769.x.
324
Green PN, Ardley JK. Review of the genus Methylobacterium and closely related
325
organisms: a proposal that some Methylobacterium species be reclassified into a new
326
genus, Methylorubrum gen. nov. Int J Syst Evol Microbiol 2018;68:2727-48.
327
https://doi.org/10.1099/ijsem.0.002856.
328
Guenther A. The contribution of reactive carbon emissions from vegetation to the
329
carbon balance of terrestrial ecosystems. Chemosphere 2002;49:837-44.
330
https://doi.org/10.1016/s0045-6535(02)00384-3.
331
Henrot AJ, Stanelle T, Schroder S et al. Implementation of the MEGAN (v2.1) biogenic
332
emission model in the ECHAM6-HAMMOZ chemistry climate model. Geosci
333
Model Dev 2017;10:903-26. https://doi.org/10.5194/gmd-10-903-2017.
334
Iguchi H, Sato I, Sakakibara M et al. Distribution of methanotrophs in the phyllosphere.
335
Biosci Biotechnol Biochem 2012;76:1580-83. https://doi.org/10.1271/bbb.120281.
336
Iguchi H, Sato I, Yurimoto H et al. Stress resistance and C1 metabolism involved in
13
337
plant colonization of a methanotroph Methylosinus sp. B4S. Arch Microbiol
338
2013;195:717-26. https://doi.org/10.1007/s00203-013-0922-6.
339
Iguchi H, Umeda R, Taga H et al. Community composition and methane oxidation
340
activity of methanotrophs associated with duckweeds in a fresh water lake. J Biosci
341
Bioeng 2019;128:450-5. https://doi.org/10.1016/j.jbiosc.2019.04.009.
342
Iguchi H, Yoshida Y, Fujisawa K et al. KaiC family proteins integratively control
343
temperature-dependent UV resistance in Methylobacterium extorquens AM1.
344
Environ Microbiol Rep 2018;10:634-43. https://doi.org/10.1111/1758-2229.12662.
345
Ikeda S, Anda M, Inaba S et al. Autoregulation of nodulation interferes with impacts of
346
nitrogen fertilization levels on the leaf-associated bacterial community in soybeans.
347
Appl Environ Microbiol 2011;77:1973-80. https://doi.org/10.1128/AEM.02567-10.
348
349
350
351
352
Johnson CH, Mori T, Xu Y. A cyanobacterial circadian clockwork. Curr Biol
2008;18:R816-25. https://doi.org/10.1016/j.cub.2008.07.012.
Johnson CH, Zhao C, Xu Y et al. Timing the day: what makes bacterial clocks tick? Nat
Rev Microbiol 2017;15:232-42. https://doi.org/10.1038/nrmicro.2016.196.
Kawaguchi K, Yurimoto H, Oku M et al. Yeast methylotrophy and autophagy in a
353
methanol-oscillating environment on growing Arabidopsis thaliana leaves. PLoS
354
One 2011;6:e25257. https://doi.org/10.1371/journal.pone.0025257.
355
Keppler F, Hamilton JTG, Brass M et al. Methane emissions from terrestrial plants
356
under aerobic conditions. Nature. 2006;439:187-91.
357
https://doi.org/10.1038/Nature04420.
358
Kirschbaum MUF, Bruhn D, Etheridge DM et al. A comment on the quantitative
359
significance of aerobic methane release by plants. Funct Plant Biol 2006;33:521-30.
360
https://doi.org/10.1071/Fp06051.
361
362
363
364
365
Kirschke S, Bousquet P, Ciais P et al. Three decades of global methane sources and
sinks. Nat Geosci 2013;6:813-23. https://doi.org/10.1038/Ngeo1955.
Knief C. Diversity of methane cycling microorganisms in soils and their relation to
oxygen. Curr Issues Mol Biol 2019;33:23-56. https://doi.org/10.21775/cimb.033.023.
Knief C, Delmotte N, Chaffron S et al. Metaproteogenomic analysis of microbial
366
communities in the phyllosphere and rhizosphere of rice. ISME J 2012;6:1378-90.
367
https://doi.org/10.1038/ismej.2011.192.
14
368
Knief C, Ramette A, Frances L et al. Site and plant species are important determinants
369
of the Methylobacterium community composition in the plant phyllosphere. ISME J
370
2010;4:719-28. https://doi.org/10.1038/ismej.2010.9.
371
Kumar M, Tomar RS, Lade H et al. Methylotrophic bacteria in sustainable agriculture.
372
World J Microbiol Biotechnol 2016;32:120. https://doi.org/10.1007/s11274-016-
373
2074-8.
374
Kumar M, Kour D, Yadav AN et al. Biodiversity of methylotrophic microbial
375
communities and their potential role in mitigation of abiotic stresses in plants.
376
Biologia 2019;74:287-308. https://doi.org/10.2478/s11756-019-00190-6.
377
378
Lindow SE, Brandl MT. Microbiology of the phyllosphere. Appl Environ Microbiol
2003;69:1875-83. https://doi.org/10.1128/aem.69.4.1875-1883.2003.
379
Madhaiyan M, Poonguzhali S, Senthilkumar M et al. Growth promotion and induction
380
of systemic resistance in rice cultivar Co-47 (Oryza sativa L.) by Methylobacterium
381
spp. Bot Bull Acad Sinica 2004;45:315–24.
382
Madhaiyan M, Poonguzhali S, Sundaram SP et al. A new insight into foliar applied
383
methanol influencing phylloplane methylotrophic dynamics and growth promotion of
384
cotton (Gossypium hirsutum L.) and sugarcane (Saccharum officinarum L.). Environ
385
Exp Bot 2006;57:168-76. https://doi.org/10.1016/j.envexpbot.2005.05.010.
386
Meena KK, Kumar M, Kalyuzhnaya MG et al. Epiphytic pink-pigmented
387
methylotrophic bacteria enhance germination and seedling growth of wheat (Triticum
388
aestivum) by producing phytohormone. Antonie van Leeuwenhoek 2012;101:777-86.
389
https://doi.org/10.1007/s10482-011-9692-9.
390
Mercier J, Lindow SE. Role of leaf surface sugars in colonization of plants by bacterial
391
epiphytes. Appl Environ Microbiol 2000;66:369-74.
392
https://doi.org/10.1128/AEM.66.1.369-374.2000.
393
Mizuno M, Yurimoto H, Iguchi H et al. Dominant colonization and inheritance of
394
Methylobacterium sp. strain OR01 on perilla plants. Biosci Biotechnol Biochem
395
2013;77:1533-8. https://doi.org/10.1271/bbb.130207.
396
Mizuno M, Yurimoto H, Yoshida N et al. Distribution of pink-pigmented facultative
397
methylotrophs on leaves of vegetables. Biosci Biotechnol Biochem 2012;76:578-80.
398
https://doi.org/10.1271/bbb.110737.
15
399
Nemecek-Marshall M, Macdonald RC, Franzen FJ et al. Methanol emission from
400
leaves: enzymatic detection of gas-phase methanol and relation of methanol fluxes to
401
stomatal conductance and leaf development. Plant Physiol 1995;108:1359-68.
402
https://doi.org/10.1104/pp.108.4.1359.
403
Ortiz-Castro R, Contreras-Cornejo HA, Macias-Rodriguez L et al. The role of microbial
404
signals in plant growth and development. Plant Signal Behav 2009;4:701-12.
405
https://doi.org/10.4161/psb.4.8.9047
406
Parsons AJ, Newton PCD, Clark H et al. Scaling methane emissions from vegetation.
407
Trends Ecol Evol 2006;21:423-4. https://doi.org/10.1016/j.tree.2006.05.017.
408
Rodionov DA, Hebbeln P, Eudes A et al. A novel class of modular transporters for
409
vitamins in prokaryotes. J Bacteriol 2009;191:42-51.
410
https://doi.org/10.1128/JB.01208-08.
411
Ryback B, Bortfeld-Miller M, Vorholt JA. Metabolic adaptation to vitamin auxotrophy
412
by leaf-associated bacteria. ISME J 2022; 16:2712-2724.
413
https://doi.org/10.1038/s41396-022-01303-x
414
Ryu J, Madhaiyan M, Poonguzhali S et al. Plant growth substances produced by
415
Methylobacterium spp. and their effect on tomato (Lycopersicon esculentum L.) and
416
red pepper (Capsicum annuum L.) growth. J Microbiol Biotechnol 2006;16:1622-8.
417
Saunois M, Bousquet P, Poulter B et al. The global methane budget 2000-2012. Earth
418
Syst Sci Data 2016;8:697-751. https://doi.org/10.5194/essd-8-697-2016.
419
Schmidt S, Christen P, Kiefer P et al. Functional investigation of methanol
420
dehydrogenase-like protein XoxF in Methylobacterium extorquens AM1.
421
Microbiology 2010;156:2575-86. https://doi.org/10.1099/mic.0.038570-0.
422
Schrader J, Schilling M, Holtmann D et al. Methanol-based industrial biotechnology:
423
current status and future perspectives of methylotrophic bacteria. Trends Biotechnol
424
2009;27:107-15. https://doi.org/10.1016/j.tibtech.2008.10.009.
425
Sy A, Timmers AC, Knief C et al. Methylotrophic metabolism is advantageous for
426
Methylobacterium extorquens during colonization of Medicago truncatula under
427
competitive conditions. Appli Environ Microbiol 2005;71:7245-52.
428
https://doi.org/10.1128/AEM.71.11.7245-7252.2005.
429
Yang CH, Crowley DE, Borneman J et al. Microbial phyllosphere populations are more
16
430
complex than previously realized. Proc Natl Acad Sci USA 2001;98:3889-94.
431
https://doi.org/10.1073/pnas.051633898.
432
Yoshida N, Iguchi H, Yurimoto H et al. Aquatic plant surface as a niche for
433
methanotrophs. Front Microbiol 2014;5:30.
434
https://doi.org/10.3389/Fmicb.2014.00030.
435
Yoshida Y, Iguchi H, Sakai Y et al. Pantothenate auxotrophy of Methylobacterium spp.
436
isolated from living plants. Biosci Biotechnol Biochem 2019;83:569-77.
437
https://doi.org/10.1080/09168451.2018.1549935.
438
Yurimoto H, Shiraishi K, Sakai Y. Physiology of methylotrophs living in the
439
phyllosphere. Microorganisms 2021;9:809.
440
https://doi.org/10.3390/microorganisms9040809
441
Yurimoto H, Iguchi H, Di Thien DT et al. Methanol bioeconomy: promotion of rice
442
crop yield in paddy fields with microbial cells prepared from natural gas-derived C1
443
compound. Microb Biotechnol 2021;14:1385-96. https://doi.org/10.1111/1751-
444
7915.13725.
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Figure legends
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Figure 1. The global carbon cycle mediated by C1-miroorganisms and plants. Methane is
448
generated from CO2 by methanogens and C1-microorganisms including methanotrophs
449
and methanol-utilizing methylotrophs oxidize methane and other C1 compounds to
450
CO2. This cycle is known as methane cycle. Recently, C1-microorganisms in the
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phyllosphere were found to utilize methane and methanol produced by plants. Positive
452
interactions between PPFMs and plants enhance CO2 fixation and increase plant
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biomass (yield increase).
454
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Figure 2. Interactions between PPFMs and plants in the phyllosphere. PPFMs utilize
456
nutrients such as methanol as a carbon source and other cofactors such as vitamins.
457
PPFMs provide benefit to plants by producing plant hormones, enhancing nutrient
458
uptake of plants, and inducing resistance to pathogens. PPFMs have various cellular
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functions for adapting to diurnally changing environmental factors in the phyllosphere.
460
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Figure 3. Summary of the effects of PPFM treatment on rice crop yields (cultivar
462
Hakutsurunishiki). Graphs were replotted from the previously reported data (Yurimoto
463
et al. 2021). (a) The weight of brown rice in a commercial paddy field in 2017
464
following the indicated treatments. (b and c) The rate of ripening (b) and the unit yield
465
466
(c) in 2018 after the indicated treatments.
18
C1-microorganisms
Methane
cycle
CH4
CH3OH
HCHO
Emission
P la n t
b io m a s s
sio
Em
PPFMs
Plants
Yield increase
HCOOH
Methanogens
CO2
Plants
CO2 fixation
Degradation
Fig. 1
Nutrients (methanol, sugars, etc.)
Vitamins and their precursors
PPFMs
Adaptation to diurnally changing
environmental factors
Benefit
Plant hormones, Nutrient uptake,
Resistance to pathogens
Fig. 2
(a)
Cell wall polysaccharide fraction
Killed cells
Living cells
Control (spreading agent)
66
68
70
72
Weight of brown rice (Kg/a)
(b)
Killed cells after heading
Killed cells before heading
Killed cells before and after heading
Control (spreading agent)
68
(c)
72
76
80
Rate of ripening (%)
84
Killed cells after heading
Killed cells before heading
Killed cells before and after heading
Control (spreading agent)
480 520 560 600 640 680
Unit yield (g/m2)
Fig. 3
...