Physiology, biochemistry, and specific inhibitors of CH4, NH4+, and CO oxidation by methanotrophs and nitrifiers.

Bédard, Charles; Knowles, Roger

doi:10.1128/mmbr.53.1.68-84.1989

Cited by 585 publications

(388 citation statements)

References 106 publications

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“…Michaelis-Menten kinetics of atmospheric CH4 oxidation in upland soil samples were reported in the early 1990s and the observed Km(app) values were in the nanomolar range (Bender and Conrad, 1992;1993;. To that date reported Km(app) values of cultivated methanotrophic species were above 1 mM (Bedard and Knowles, 1989), and comparable values could only be measured in aerated soils when the respective sample was preincubated at concentrations above 50 000 ppmv CH4 (Bender and Conrad, 1992). Furthermore, aqueous extracts containing methanotrophic cells from several acidic forest soils displayed CH4 oxidation optima at pH 5.8 and were not able to oxidize atmospheric CH4 mixing ratios at pH 7.0.…”

Section: The Beginning Of the Questmentioning

confidence: 97%

The quest for atmospheric methane oxidizers in forest soils

Kolb

2009

Environ Microbiol Rep

196

175

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Aerobic methanotrophs in forest soils are the largest biological sink for atmospheric methane (CH4 ). Community structures in 53 soils from Europe, Russia, North and South America, Asia and New Zealand located in boreal, temperate and tropical forests were analysed and maximal abundances of 2.1 × 10(7) methanotrophs g(-1) DW were measured. In acidic soils, the most frequently detected pmoA genotypes were Upland Soil Cluster α (USCα) and Methylocystis spp. Phospholipid fatty acids that were labelled by consumption of (14/13) CH4 suggested the activity of type II methanotrophs. Cluster 1 (Methylocystaceae), USCγ and Methylocystis spp. were frequently detected genotypes in pH-neutral soils. Genotypes with ambiguous functional affiliation were co-detected (Clusters MR1, RA21, 2) and may represent aerobic methanotrophs, ammonia oxidizers or enzymes with an unknown function. The physiological traits of atmospheric CH4 oxidizers are largely unknown because organisms possessing the key forest soil pmoA genotypes (USCα, USCγ, Cluster 1) have not been cultivated. Some methanotrophic strains belonging to the family Methylocystaceae have been shown to oxidize CH4 at atmospheric mixing ratios. Methylocystis strain SC2 was found to have an alternative particulate CH4 monooxygenase responsible for CH4 oxidation at atmospheric mixing ratios. pH, forest type and temperature might be environmental factors that shape methanotrophic communities in forest soils. However, specific effects on individual species are largely unknown, and only a limited number of studies have addressed environmental controls of methanotrophic diversity, pointing to the need for future research in this area.

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Section: The Beginning Of the Questmentioning

confidence: 97%

The quest for atmospheric methane oxidizers in forest soils

Kolb

2009

Environ Microbiol Rep

196

175

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“…The response of methanotrophs to nitrogen has been a major subject of study because of the potential for inhibition of methanotrophs by ammonium and/or nitrite (Hanson and Hanson, 1996). Numerous studies have shown, using pure cultures, microcosms and field trials, that nitrogen additions decrease methane oxidation (Bedard and Knowles, 1989;Conrad and Rothfuss, 1991). On the other hand, recent rice microcosm studies (Bodelier and Frenzel, 1999;Bodelier et al, 2000) have clearly shown that N fertilization increases methane oxidation in densely rooted rice soil.…”

Section: Effect Of Rice Plants On Methanotroph Populationsmentioning

confidence: 99%

Population dynamics of type I and II methanotrophic bacteria in rice soils

Macalady

McMillan

Dickens

et al. 2002

Environmental Microbiology

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Methane-oxidizing bacteria (methanotrophs) consume a significant but variable fraction of greenhouse-active methane gas produced in wetlands and rice paddies before it can be emitted to the atmosphere. Temporal and spatial dynamics of methanotroph populations in California rice paddies were quantified using phospholipid biomarker analyses in order to evaluate the relative importance of type I and type II methanotrophs with depth and in relation to rice roots. Methanotroph population fluctuations occurred primarily within the top 0-2 cm of soil, where methanotroph cells increased by a factor of 3-5 over the flooded rice-growing season. The results indicate that rice roots and rhizospheres were less important than the soil-water interface in supporting methanotroph growth. Both type I and type II methanotrophs were abundant throughout the year. However, only type II populations were strongly correlated with soil porewater methane concentrations and rice growth.

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“…However, AMO is much less efficient than MMO in CH 4 oxidation, so about a thousand AOB cells are needed to achieve the same rate of CH 4 oxidation as a single MB cell (Jiang and Bakken, 1999). Thus, AOB apparently do not play an important role in CH 4 uptake by soils (Bedard and Knowles, 1989;Bender and Conrad, 1994;Bodelier and Frenzel, 1999). Bender and Conrad (1992) first suggested that the MB active in upland soils were not known species.…”

Section: Introductionmentioning

confidence: 99%

Abundance and activity of uncultured methanotrophic bacteria involved in the consumption of atmospheric methane in two forest soils

Kolb¹,

Knief²,

Dunfield³

et al. 2005

Environmental Microbiology

175

154

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The activity and abundance of methanotrophic bacteria were measured in an acidic and a neutral forest soil. The soils exhibited high uptake rates (>30 microg CH4 m(-2) h(-1)) of atmospheric CH4 at all measurement times throughout the vegetation period. The abundances of various phylogenetic groups of methanotrophs, including some uncultured putative ones, were measured using real-time polymerase chain reaction assays. Each assay specifically targeted the pmoA gene or mmoX gene of a particular group of methanotrophs, or the amoA gene of ammonia-oxidizing bacteria. As yet uncultured methanotrophs of a group previously named 'forest soil cluster' or 'USC alpha' were numerically dominant in the acidic soil, while cultured but taxonomically uncharacterized methanotrophs of a group 'Cluster I' were dominant in the neutral soil. Each group was detected in numbers equivalent to about 10(6) pmoA gene copies per gram dry weight of soil and comprised >90% of the detectable methanotrophic bacteria in the respective soil. As the numbers of ammonia-oxidizing bacteria were similar but not higher, they could not have accounted for the observed CH4 uptake rates due to their low cell-specific CH4 oxidation activity. Based on CH4 flux and bacterial abundance data, estimated cell-specific CH4 oxidation rates of the detected methanotrophic bacteria were 540-800 x 10(-18) mol cell(-1) h(-1), which is high compared with literature values of cultured methanotrophic bacteria. These estimated cell-specific CH4 oxidation rates are sufficiently high to allow not only maintenance but even growth on atmospheric CH4 alone. Transcripts of mRNA of the pmoA gene were detected in the acidic soil, demonstrating that USC alpha methanotrophs expressed pmoA under ambient methane mixing ratios. On the other hand, pmoA transcripts of Cluster I or of other methanotrophic groups were not detectable. Our study suggests that USC alpha and Cluster I methanotrophs are adapted to the low concentration of methane in forest soils by possessing high cell-specific CH4 oxidation activities.

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Physiology, biochemistry, and specific inhibitors of CH4, NH4+, and CO oxidation by methanotrophs and nitrifiers.

Cited by 585 publications

References 106 publications

The quest for atmospheric methane oxidizers in forest soils

The quest for atmospheric methane oxidizers in forest soils

Population dynamics of type I and II methanotrophic bacteria in rice soils

Abundance and activity of uncultured methanotrophic bacteria involved in the consumption of atmospheric methane in two forest soils

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