Skip to main content

Advertisement

SpringerLink
Log in

Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments

  • Original Paper
  • Published:
Archives of Microbiology Aims and scope Submit manuscript

Abstract

One-carbon compounds such as methanol, dimethylsulfide (DMS) and dimethylsulfoxide (DMSO) are significant intermediates in biogeochemical cycles. They are suggested to affect atmospheric chemistry and global climate. Methylotrophic microorganisms are considered as a significant sink for these compounds; therefore, we analyzed the diversity of terrestrial bacteria that utilize methanol, DMS and DMSO as carbon and energy source using culture-dependent and culture-independent methods. The effect of habitat type on the methylotrophic community structure was also investigated in rhizosphere and bulk soil. While thirteen strains affiliated to the genera Hyphomicrobium, Methylobacterium, Pseudomonas, Hydrogenophaga, Rhodococcus, Flavobacterium and Variovorax were isolated, denaturing gradient gel electrophoresis revealed the dominance of Thiobacillus, Rhodococcus, Flavobacterium and Bacteroidetes species. Furthermore, methylotrophic communities that degrade methanol or DMS are not shaped by terrestrial habitat type. Rhizosphere and soil samples showed dominance of Methylophilus spp. and Methylovorus spp. for methanol enrichments; Cytophaga spp., Pseudomonas tremae and Thiobacillus thioparus for DMS enrichments.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  PubMed  CAS  Google Scholar 

  • Anthony C (1982) The biochemistry of methylotrophs. Academic Press, London

    Google Scholar 

  • Bending GD, Lincoln SD (1999) Characterisation of volatile sulphur-containing compounds produced during decomposition of Brassica juncea tissues in soil. Soil Biol Biochem 31:695–703

    Article  CAS  Google Scholar 

  • Boden R, Thomas E, Savani P, Kelly DP, Wood AP (2008) Novel methylotrophic bacteria isolated from the River Thames (London, UK). Environ Microbiol 10:3225–3236

    Article  PubMed  Google Scholar 

  • Borodina E, Kelly DP, Rainey FA, Ward-Rainey NL, Wood AP (2000) Dimethylsulfone as a growth substrate for novel methylotrophic species of Hyphomicrobium and Arthrobacter. Arch Microbiol 173:425–437

    Article  PubMed  CAS  Google Scholar 

  • Chanprame S, Todd JJ, Widholm JM (1996) Prevention of pink-pigmented methylotrophic bacteria (Methylobacterium mesophilicum) contamination of plant tissue cultures. Plant Cell Rep 16:222–225

    Article  PubMed  CAS  Google Scholar 

  • Charlson RJ, Lovelock JE, Andreae MO, Warren SG (1987) Oceanic phytoplankton, atmospheric sulphur, cloud albedo and climate. Nature 326:655–661

    Article  CAS  Google Scholar 

  • Chistoserdova L, Kalyuzhnaya MG, Lidstrom ME (2009) The expanding world of methylotrophic metabolism. Annu Rev Microbiol 63:477–499

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Corpe WA, Rheem S (1989) Ecology of the methylotrophic bacteria on living leaf surfaces. FEMS Microbiol Ecol 62:243–249

    Article  CAS  Google Scholar 

  • Crocco JR (1994) Global outlook: supply, demand, and marketing. In: Cheng WH, Kung K (eds) Methanol production and use. Marcel Dekker, New York, pp 283–317

    Google Scholar 

  • Crocco JR (1997) World methanol demand forecast to grow 2.7% over five years. Hydrocarbon Process 76:25

    Google Scholar 

  • De Bont JAM, van Dijken JP, Harder W (1981) Dimethyl sulphoxide and dimethyl sulphide as a carbon, sulphur and energy source for growth of Hyphomicrobium S. J Gen Microbiol 127:315–323

    Google Scholar 

  • Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, von Mering C, Vorholt JA (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. PNAS 106:16428–16433

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Duineveld BM, Kowalchuk GA, Keijzer A, van Elsas JD, van Veen JA (2001) Analysis of bacterial communities in the rhizosphere of Chrysanthemum via denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA as well as DNA fragments coding for 16S rRNA. Appl Environ Microbiol 67(1):172–178

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Eyice O, Namura M, Chen Y, Mead A, Samavedam S, Schäfer H (2015) SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment. ISME J. doi:10.1038/ismej.2015.37

    PubMed  PubMed Central  Google Scholar 

  • Galbally IE, Kirstine W (2002) The production of methanol by flowering plants and the global cycle of methanol. J Atmos Chem 43:195–229

    Article  CAS  Google Scholar 

  • Gamliel A, Stapleton JJ (1993) Characterization of antifungal volatile compounds evolved from solarized soil amended with cabbage residues. Phytopathology 83:899–905

    Article  CAS  Google Scholar 

  • Ginige MP, Bowyer JC, Foley L, Keller J, Yuan Z (2009) A comparative study of methanol as a supplementary carbon source for enhancing denitrification in primary and secondary anoxic zones. Biodegradation 20:221–234

    Article  PubMed  CAS  Google Scholar 

  • Giri BS, Juwarkar AA, Satpute DP, Mudliar SN, Pandey RA (2012) Isolation and characterization of dimethylsulfide (DMS)-degrading bacteria from soil and biofilter treating waste gas containing DMS from the laboratory and pul and paper industry. Appl Biochem Biotechnol 167:1744–1752

    Article  PubMed  CAS  Google Scholar 

  • Gogleva AA, Kaparullina EN, Doronina NV, Trotsenko YA (2010) Methylophilus flavus sp. nov. and Methylophilus luteus sp. nov., aerobic, methylotrophic bacteria associated with plants. J Syst Evol Microbiol 60:2623–2628

    Article  CAS  Google Scholar 

  • Hayes A, Zhang Y, Liss S, Allen D (2010) Linking performance to microbiology in biofilters treating dimethyl sulphide in the presence and absence of methanol. Appl Microbiol Biotechnol 85:1151–1166

    Article  PubMed  CAS  Google Scholar 

  • Hirano SS, Upper CD (1991) Bacterial community dynamics. In: Andrews JH, Hirano SS (eds) Microbial ecology on leaves. Springer, New York, pp 271–294

    Chapter  Google Scholar 

  • Holm NC, Gliesche CG, Hirsch P (1996) Diversity and structure of Hyphomicrobium populations in a sewage treatment plant and its adjacent receiving lake. Appl Environ Microbiol 62:522–528

    PubMed  CAS  PubMed Central  Google Scholar 

  • Johnson DB, Macvicar JHM, Rolfe S (1987) A new solid medium for the isolation and enumeration of Thiobacillus ferrooxidans and acidophilic heterotrophic bacteria. J Microbiol Methods 7:9–18

    Article  Google Scholar 

  • Kalyuzhnaya MG, Hristova KR, Lidstrom ME, Chistoserdova L (2008) Characterization of a novel methanol dehydrogenase in representatives of Burkholderiales: implications for environmental detection of methylotrophy and evidence for convergent evolution. J Bacteriol 190:3817–3823

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Kalyuzhnaya MG, Martens-Habbena W, Wang T, Hackett M, Stolyar SM, Stahl DA, Lidstrom ME, Chistoserdova L (2009) Methylophilaceae link methanol oxidation to denitrification in freshwater lake sediment as suggested by stable isotope probing and pure culture analysis. Environ Microbiol Rep 1:385–392

    Article  Google Scholar 

  • Kanagawa T, Kelly DP (1986) Breakdown of dimethyl sulfide by mixed cultures and by Thiobacillus thioparus. FEMS Microbiol Lett 34:13–19

    Article  CAS  Google Scholar 

  • Kertesz MA, Mirleau P (2004) The role of soil microbes in plant sulphur nutrition. J Exp Bot 55:1939–1945

    Article  PubMed  CAS  Google Scholar 

  • Khadem AF, Pol A, Wieczorek A, Mohammadi SS et al (2011) Autotrophic methanotrophy in Verrumicrobia: Methylacidiphilum fumariolicum SoIV uses the Calvin–Benson–Bassham cycle for carbon dioxide fixation. J Bacteriol 193:4438–4446

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Kiene RP, Hines ME (1995) Microbial formation of dimethyl sulfide in anoxic Sphagnum peat. Appl Environ Microbiol 61:2720–2726

    PubMed  CAS  PubMed Central  Google Scholar 

  • Kim TG, Lee E-H, Cho K-S (2013) Effects of nonmethane volatile organic compounds on microbial community of methanotrophic biofilter. Appl Microbiol Biotechnol 97:6549–6559

    Article  PubMed  CAS  Google Scholar 

  • Knief C, Ramette A, Frances L, Alonso-Blanco C, Vorholt JA (2010) Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere. ISME J 4:719–728

    Article  PubMed  CAS  Google Scholar 

  • Kolb S (2009) Aerobic methanol-oxidizing bacteria in soil. FEMS Microbiol Lett 300:1–10

    Article  PubMed  CAS  Google Scholar 

  • Kolb S, Stacheter A (2013) Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment. Front Microbiol 4:1–12

    Article  Google Scholar 

  • Lane DJ (1991) 16S/23S rRNA Sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–175

    Google Scholar 

  • Lindow SE, Brandl MT (2003) Microbiology of the phyllosphere. Appl Environ Microbiol 69:1875–1883

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Lomans BP, Smolders AJP, Intven LM, Pol A, Op Den Camp HJM, Van Der Drift C (1997) Formation of dimethyl sulfide and methanethiol in anoxic freshwater sediments. Appl Environ Microbiol 63:4741–4747

    PubMed  CAS  PubMed Central  Google Scholar 

  • Lomans BP, Luderer R, Steenbakkers P, Pol A, van der Drift C, Vogels GD et al (2001) Microbial populations involved in cycling of dimethyl sulfide and methanethiol in freshwater sediments. Appl Environ Microbiol 67:1044–1051

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Ludwig W, Strunk O, Westram R, Richter L, Meier H et al (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Lueders T, Wagner B, Claus P, Friedrich MW (2004) Stable isotope probing of rRNA and DNA reveals a dynamic methylotroph community and trophic interactions with fungi and protozoa in oxic rive field soil. Environ Microbiol 6:60–72

    Article  PubMed  CAS  Google Scholar 

  • MacDonald RC, Fall R (1993) Detection of substantial emissions of methanol from plants to the atmosphere. Atmos Environ 27:1709–1713

    Article  Google Scholar 

  • Mano H, Tanaka F, Nakamura C, Kaga H, Morisaki H (2007) Culturable endophytic bacterial flora of the maturing leaves and roots of rice plants (Oryza sativa) cultivated in a paddy field. Microbiol Environ 22:175–185

    Article  Google Scholar 

  • Muyzer G, Brinkhoff T, Nübel U, Santegoeds C, Schäfer H, Waver C (1998) Denaturing gradient gel electrophoresis (DGGE) in microbial ecology. In: Akkermans ADL, van Elsas JD, de Bruijn FJ (eds) Molecular microbial ecology manual. Kluwer Academic Publishers, Dordrecht, pp 1–27

    Google Scholar 

  • Nadalig T, Ul Haque MF, Roselli S, Schaller H, Bringel F, Vuilleumier S (2011) Detection and isolation of chloromethane-degrading bacteria from the Arabidopsis thaliana phyllosphere, and characterization of chloromethane utilization genes. FEMS Microbiol Lett 77:438–448

    Article  CAS  Google Scholar 

  • Nemecek-Marshall M, MacDonald RC, Franzen JJ, Wojciechowski CL, Fall R (1995) Methanol emission from leaves (enzymatic detection of gas-phase methanol and relation of methanol fluxes to stomatal conductance and leaf development). Plant Physiol 108(4):1359–1368

    PubMed  CAS  PubMed Central  Google Scholar 

  • Nercessian O, Noyes E, Kalyuzhnaya MG, Lidstrom ME, Chistoserdova L (2005) Bacterial populations active in metabolism of C1 compounds in the sediment of lake Washington, a freshwater lake. Appl Environ Microbiol 71:6885–6899

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Normander B, Prosser JI (2000) Bacterial origin and community composition in the barley phytosphere as a function of habitat and presowing conditions. Appl Environ Microbiol 66(10):4372–4377

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Omori T, Saiki Y, Kasuga K, Kodama T (1995) Desulfurization of alkyl and aromatic sulfides and sulfonates by dibenzothiophene-desulfurizing Rhodococcus sp. strain Sy1. Biosci Biotechnol Biochem 59:1195–1198

    Article  CAS  Google Scholar 

  • Pearson TW, Dawson HJ, Lackey HB (1981) Natural occurring levels of dimethyl sulfoxide in selected fruits, vegetables, grains and beverages. J Agric Food Chem 29:1089–1091

    Article  PubMed  CAS  Google Scholar 

  • Pol A, Op den Camp HJM, Mees SGM, Kersten MASH, van der Drift C (1994) Isolation of a dimethylsulfide-utilizing Hyphomicrobium species and its application in biofiltration of polluted air. Biodegradation 5:105–112

    Article  PubMed  CAS  Google Scholar 

  • Radajewski S, Webster G, Reay DS, Morris SA, Ineson P, Nedwell DB et al (2002) Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing. Microbiology 148:2331–2342

    Article  PubMed  CAS  Google Scholar 

  • Roesch LFW, Fulthorpe RR, Riva A, Casella G et al (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290

    PubMed  CAS  PubMed Central  Google Scholar 

  • Scarlata CJ, Ebeler SE (1999) Headspace solid-phase microextraction for the analysis of dimethyl sulfide in beer. J Agric Food Chem 47:2505–2508

    Article  PubMed  CAS  Google Scholar 

  • Schäfer H, Muyzer G (2001) Denaturing gradient gel electrophoresis in marine microbial ecology. In: Paul JH (ed) Methods in microbiology. Academic Press, London, pp 425–468

    Google Scholar 

  • Schäfer H, Miller L, Oremland R, Murrell JC (2007) Bacterial cycling of methyl halides. In: Laskin AI, Sariaslani S, Gadd G (eds) Adv Appl Microbiol 61:307–346

  • Schäfer H, Myronova N, Boden R (2010) Microbial degradation of dimethylsulfide and related C1-sulfur compounds: organisms and pathways controlling fluxes of sulfur in the biosphere. J Exp Bot 61:315–334

    Article  PubMed  Google Scholar 

  • Sivelä S, Sundman V (1975) Demonstration of Thiobacillus type bacteria, which utilize methyl sulfides. Arch Microbiol 103:303–304

    Article  Google Scholar 

  • Smith NA, Kelly DP (1988) Isolation and physiological characterization of autotrophic sulphur bacteria oxidizing dimethyl disulfide as sole source of energy. J Gen Microbiol 134:1407–1417

    CAS  Google Scholar 

  • Stacheter A, Noll M, Lee CK, Selzer M et al (2013) Methanol oxidation by temperate soils and environmental determinants of associated methylotrophs. ISME J 7:1051–1064

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Steeghs M, Bais HP, de Gouw J, Goldan P, Kuster W, Northway M, Fall R, Vivanco JM (2004) Proton-transfer-reaction mass spectrometry as a new tool for real time analysis of root-secreted volatile organic compounds in Arabidopsis. Plant Physiol 135:47–58

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Suylen GMH, Kuenen JG (1986) Chemostat enrichment and isolation of Hyphomicrobium EG a dimethyl sulfide oxidizing methylotroph and reevaluation of Thiobacillus MS1. Antonie Van Leeuwenhoek 52:281–293

    Article  PubMed  CAS  Google Scholar 

  • Trotsenko YA, Murrell JC (2008) Metabolic aspects of aerobic obligate methanotrophy. Adv Appl Microbiol 63:183–229

    Article  PubMed  CAS  Google Scholar 

  • Turner TR, Ramakrishnan K, Walshaw J, Heavens D et al (2013) Comparative metatrascriptomics reveals kingdom level changes in the rhizosphere microbiome of plants. ISME J 7:2248–2258

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev 10:828–840

    CAS  Google Scholar 

  • Watts SF (2000) The mass budgets of carbonyl sulfide, dimethyl sulfide, carbon disulfide and hydrogen sulfide. Atmos Environ 34:761–779

    Article  CAS  Google Scholar 

  • Wellner S, Lodders N, Kämpfer P (2011) Diversity and biogeography of selected phyllosphere bacteria with special emphasis on Methylobacterium spp. Syst Appl Microbiol 34:621–630

    Article  PubMed  CAS  Google Scholar 

  • Whitfield WAD (1974) The soils of the national vegetable research station, Wellesbourne. Report of the National Vegetable Research Station for 1973, pp 21–30

  • Wood AP, Kelly DP (1977) Heterotrophic growth of Thiobacillus A2 on sugars and organic acids. Arch Microbiol 113:257–264

    Article  PubMed  CAS  Google Scholar 

  • Zhang Y, Liss SN, Allen DG (2006) The effects of methanol on the biofiltration of dimethyl sulfide in inorganic biofilters. Biotechnol Bioeng 95:734–743

    Article  PubMed  CAS  Google Scholar 

  • Zinder SH, Brock TD (1978) Dimethyl sulphoxide reduction by microorganisms. J Gen Microbiol 105:335–342

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

H.S. was supported by UK Natural Environment Research Council Grant NE/E013333/1), and Ö.E. was supported by a postgraduate scholarship from School of Life Sciences, University of Warwick, UK. Kevin Purdy is acknowledged for insightful comments on the manuscript.

Author information

Authors and Affiliations

  1. School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK

    Özge Eyice & Hendrik Schäfer

Authors
  1. Özge Eyice
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hendrik Schäfer
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Özge Eyice or Hendrik Schäfer.

Ethics declarations

Conflict of interest

None.

Additional information

Communicated by Erko Stackebrandt.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Eyice, Ö., Schäfer, H. Culture-dependent and culture-independent methods reveal diverse methylotrophic communities in terrestrial environments. Arch Microbiol 198, 17–26 (2016). https://doi.org/10.1007/s00203-015-1160-x

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00203-015-1160-x

Keywords

Search

Navigation