Kumaresan, Deepak, Stralis-Pavese, Nancy, Abell, Guy C. J., Bodrossy, Levente and Murrell, J. Colin. (2011) Physical disturbance to ecological niches created by soil structure alters community composition of methanotrophs. Environmental Microbiology Reports, Volume 3 (Number 5). pp. 613-621. ISSN 1758-2229

Full text not available from this repository.

Abstract

Aggregates of different sizes and stability in soil create a composite of ecological niches differing in terms of physico-chemical and structural characteristics. The aim of this study was to identify, using DNA-SIP and mRNA-based microarray analysis, whether shifts in activity and community composition of methanotrophs occur when ecological niches created by soil structure are physically perturbed. Landfill cover soil was subject to three treatments termed: 'control' (minimal structural disruption), 'sieved' (sieved soil using 2 mm mesh) and 'ground' (grinding using mortar and pestle). 'Sieved' and 'ground' soil treatments exhibited higher methane oxidation potentials compared with the 'control' soil treatment. Analysis of the active community composition revealed an effect of physical disruption on active methanotrophs. Type I methanotrophs were the most active methanotrophs in 'sieved' and 'ground' soil treatments, whereas both Type I and Type II methanotrophs were active in the 'control' soil treatment. The result emphasize that changes to a particular ecological niche may not result in an immediate change to the active bacterial composition and change in composition will depend on the ability of the bacterial communities to respond to the perturbation.

Item Type:	Journal Article
Subjects:	Q Science > QR Microbiology
Divisions:	Faculty of Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH):	Methanotrophs -- Research, Methane -- Oxidation, DNA microarrays, Soil structure, Bacteria -- Ecology -- Research, Methane -- Environmental aspects, Sanitary landfills -- Environmental aspects
Journal or Publication Title:	Environmental Microbiology Reports
Publisher:	Wiley-Blackwell Publishing Ltd.
ISSN:	1758-2229
Date:	October 2011
Volume:	Volume 3
Number:	Number 5
Page Range:	pp. 613-621
Identification Number:	10.1111/j.1758-2229.2011.00270.x
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Restricted or Subscription Access
Funder:	Natural Environment Research Council (Great Britain) (NERC), European Science Foundation (ESF), Fonds zur Förderung der Wissenschaftlichen Forschung (Austria) (FWF)
Grant number:	FP018 (ESF), I40-B06 (FWF)
References:	Abell, G.C.J., Stralis-Pavese, N., Sessitsch, A., and Bodrossy, L. (2009) Grazing affects methanotroph activity and diversity in an alpine meadow soil. Environ Microbiol Rep 1: 457–465. Amaral, J.A., and Knowles, R. (1995) Growth of methanotrophs in methane and oxygen counter gradients. FEMS Microbiol Lett 126: 215–220. Bodrossy, L., Stralis-Pavese, N., Murrell, J.C., Radajewski, S., Weilharter, A., and Sessitsch, A. (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 5: 566–582. Bodrossy, L., Stralis-Pavese, N., Konrad-Koszler, M., Weilharter, A., Reichenauer, T.G., Schofer, D., and Sessitsch, A. (2006) mRNA-based parallel detection of active methanotroph populations by use of a diagnostic microarray. Appl Environ Microbiol 72: 1672–1676. Bogner, J., Abdelrafie Ahmed, M., Diaz, C., Faaij, A., Gao, Q., Hashimoto, S., et al. (2007) Waste management. In Climate Change 2007: Mitigation Contribution of Working Group III to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Metz, B., Davidson, O.R., Bosch, P.R., Dave, R., and Meyer, L.A. (eds). Cambridge, UK, Cambridge University Press, p. 34. Borjesson, G., Sundh, I., and Svensson, B. (2004) Microbial oxidation of CH4 at different temperatures in landfill cover soils. FEMS Microbiol Ecol 48: 305–312. Buckling, A., Kassen, R., Bell, G., and Rainey, P.B. (2000) Disturbance and diversity in experimental microcosms. Nature 408: 961–964. Bussmann, I., Rahalkar, M., and Schink, B. (2006) Cultivation of methanotrophic bacteria in opposing gradients of methane and oxygen. FEMS Microbiol Ecol 56: 331–344. Cebron, A., Bodrossy, L., Chen, Y., Singer, A.C., Thompson, I.P., Prosser, J.I., and Murrell, J.C. (2007) Identity of active methanotrophs in landfill cover soil as revealed by DNA-stable isotope probing. FEMS Microbiol Ecol 62: 12–23. Chan, A.S.K., and Parkin, T.B. (2000) Evaluation of potential inhibitors of methanogenesis and methane oxidation in a landfill cover soil. Soil Biol Biochem 32: 1581–1590. Chen, Y., Dumont, M.G., Cebron, A., and Murrell, J.C. (2007) Identification of active methanotrophs in a landfill cover soil through detection of expression of 16S rRNA and functional genes. Environ Microbiol 9: 2855–2869. Chenu, C., Hassink, J., and Bloem, J. (2001) Short-term changes in the spatial distribution of microorganisms in soil aggregates as affected by glucose addition. Biol Fertil Soils 34: 349–356. Conrad, R. (1996) Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO). Microbiol Rev 60: 609–640. Crossman, Z., Abraham, F., and Evershed, R.P. (2004) Stable isotope pulse-chasing and compound specific stable carbon isotope analysis of phospholipid fatty acids to assess methane oxidizing bacterial populations in landfill cover soils. Environ Sci Technol 38: 1359–1367. Denman, K.L., Brasseur, G., Chidthaisong, A., Ciais, P., Cox, P.M., Dickinson, R.E., et al. (2007) Couplings between changes in the climate system and biogeochemistry. In Climate Change 2007: The Physical Science Basis Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Solomon, S., Qin, D., Manning, M., Chen, Z., Marquis, M., Averyt, K.B., et al. (eds). Cambridge, United Kingdom, Cambridge University Press, pp. 501–568. Dumont, M.G., and Murrell, J.C. (2005) Stable isotope probing – linking microbial identity to function. Nat Rev Microbiol 3: 499–504. Elkins, N.Z., Sabol, G.V., Ward, T.J., and Whitford, W.G. (1986) The influence of subterranean termites on the hydrological characteristics of a Chihuahuan desert ecosystem. Oecologia 68: 521–528. Focht, D.D. (1992) Diffusional constraints on microbial processes in soil. Soil Sci 154: 300–307. Gebert, J., Stralis-Pavese, N., Alawi, M., and Bodrossy, L. (2008) Analysis of methanotrophic communities in landfill biofilters using diagnostic microarray. Environ Microbiol 10: 1175–1188. Graham, D.W., Chaudhary, J.A., Hanson, R.S., and Arnold, R.G. (1993) Factors affecting competition between type I and type II methanotrophs in two-organism, continuousflow reactors. Microb Ecol 25: 1–17. Grant, R.F., and Rochette, P. (1994) Soil microbial respiration at different water potentials and temperatures: theory and mathematical modeling. Soil Sci Soc Am J 58: 1681– 1690. Greenwood, D.J., and Goodman, D. (1967) Direct measurement of the distribution of oxygen in soil aggregates and in columns of fine soil crumbs. J Soil Sci 18: 182–196. Griffiths, R.S., and Young, I.M. (1994) The effects of soil structure on protozoa in a clay-loam soil. Eur J Soil Sci 45: 285–292. Hanson, R.S., and Hanson, T.E. (1996) Methanotrophic bacteria. Microbiol Rev 60: 439–471. Hattori, T. (1973) Microbial Life in the Soil; An Introduction. New York, USA: Dekker. Henckel, T., Roslev, P., and Conrad, R. (2000) Effects of O2 and CH4 on presence and activity of the indigenous methanotrophic community in rice field soil. Environ Microbiol 2: 666–679. Héry, M., Singer, A.C., Kumaresan, D., Bodrossy, L., Stralis- Pavese, N., Prosser, J.I., et al. (2008) Effect of earthworms on the community structure of active methanotrophic bacteria in a landfill cover soil. ISME J 2: 92–104. Huber-Humer, M., Gebert, J., and Hilger, H. (2008) Biotic systems to mitigate landfill methane emissions. Waste Manage Res 26: 33–46. Im, J., Lee, S.W., Bodrossy, L., Barcelona, M.J., and Semrau, J.D. (2011) Field application of nitrogen and phenylacetylene to mitigate greenhouse gas emissions from landfill cover soils: effects on microbial community structure. Appl Microbiol Biotechnol 89: 189–200. Jones, H.A., and Nedwell, D.B. (1993) Methane emission and methane oxidation in landfill cover soil. FEMS Microbiol Lett 102: 185–195. Kumaresan, D., Abell, G.C.J., Bodrossy, L., Stralis-Pavese, N., and Murrell, J.C. (2009) Spatial and temporal diversity of methanotrophs in a landfill cover soil are differentially related to soil abiotic factors. Environ Microbiol Rep 1: 398–407. Lal, R. (1991) Soil structure and sustainability. J Sustain Agr 1: 67–92. McDonald, I.R., Bodrossy, L., Chen, Y., and Murrell, J.C. (2008) Molecular ecology techniques for the study of aerobic methanotrophs. Appl Environ Microbiol 74: 1305– 1315. Neufeld, J.D., Vohra, J., Dumont, M.G., Lueders, T., Manefield, M., Friedrich, M.W., and Murrell, J.C. (2007) DNA stable-isotope probing. Nat Protoc 2: 860–866. Op den Camp, H.J.M., Islam, T., Stott, M.B., Harhangi, H.R., Hynes, A., Schouten, S., et al. (2009) Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia. Environ Microbiol Rep 1: 293–306. Radajewski, S., Ineson, P., Parekh, N.R., and Murrell, J.C. (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403: 646–649. Rahman, M.T., Crombie, A., Chen, Y., Stralis-Pavese, N., Bodrossy, L., Meir, P., et al. (2010) Environmental distribution and abundance of the facultative methanotroph Methylocella. ISME J 5: 1061–1066. Ranjard, L., and Richaume, A. (2001) Quantitative and qualitative microscale distribution of bacteria in soil. Res Microbiol 152: 707–716. Reeburgh, W.S. (1996) ‘Soft spots’ in the global methane budget. In Microbial Growth on C1 Compounds. Lidstrom, M.E., and Tabita, F.R. (eds). Dordrecht,The Netherlands: Kluwer Academic Publishers, pp. 334–342. Renault, P., and Stengel, P. (1994) Modeling oxygen diffusion in aggregated soils: I. Anaerobiosis inside the aggregates. Soil Sci Soc Am J 58: 1017–1023. Scheutz, C., and Kjeldsen, P. (2004) Environmental factors influencing attenuation of methane and hydrochlorofluorocarbons in landfill cover soils. J Environ Qual 33: 72–79. Scheutz, C., Bogner, J., De Visscher, A., Gebert, J., Hilger, H., Huber-Humer, M., et al. (2009) Microbial Methane Oxidation Processes and Technologies for Mitigation of Landfill gas Emissions. Waste Manage Res 27: 409–455. Semrau, J.D. (2010) Current knowledge of microbial community structures in landfills and its cover soils. Appl Microbiol Biotechnol 89: 961–969. Stralis-Pavese, N., Sessitsch, A., Weilharter, A., Reichenauer, T., Riesing, J., Csontos, J., et al. (2004) Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environ Microbiol 6: 347–363. Torsvik, V., and Øvreås, L. (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5: 240–245. Trotsenko, Y.A., and Murrell, J.C. (2008) Metabolic aspects of aerobic obligate methanotrophy. Adv Appl Microbiol 63: 183–229. Uz, I., Rasche, M.E., Towsend, T., Ogram, A.V., and Lindner, A.S. (2003) Characterization of methanogenic and methanotrophic assemblages in landfill samples. Proc R Soc Lond B (Suppl) 270: S202–S205. Wardle, D.A., Verhoef, H.A., and Clarholm, M. (1998) Trophic relationships in the soil microfood-web: predicting the responses to a changing global environment. Glob Change Biol 4: 713–727. Wise, M.G., McArthur, J.V., and Shimkets, L.J. (1999) Methanotroph diversity in landfill soil: isolation of novel type I and type II methanotrophs whose presence was suggested by culture-independent 16S ribosomal DNA analysis. Appl Environ Microbiol 65: 4887–4897. Young, I.M., and Ritz, K. (1998) Can there be a contemporary ecological dimension to soil biology without a habitat? Discussion. Soil Biol Biochem 30: 1229–1232. Young, I.M., Blanchart, E., Chenu, C., Dangerfield, M., Fragoso, C., Grimaldi, M., et al. (1998) The interaction of soil biota and soil structure under global change. Glob Change Biol 4: 703–712.
URI:	http://wrap.warwick.ac.uk/id/eprint/40441

Data sourced from Thomson Reuters' Web of Knowledge

Request changes to a record

Actions (login required)

View Item