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Book ChapterDOI

The Methane-Oxidizing Bacteria (Methanotrophs)

About: The article was published on 2019-01-01. It has received 39 citations till now.
Citations
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Journal ArticleDOI
TL;DR: A high yield on methane proved that biogas is a good substitute for natural gas for scaled-up microbial protein production, and the produced SCP was rich in essential amino acids, marking the produced biomass comparable with other protein sources.

60 citations

Journal ArticleDOI
TL;DR: Soil CH4 fluxes in forests are determined by different environmental variables in different biomes, and the increase in temperature predicted in the framework of climate change would promote CH4 emission in subtropical and savannas forests, have no influence in boreal and temperate forests and promote uptake in tropical forests.
Abstract: Forest soils are the most important terrestrial sink of atmospheric methane (CH4 ). Climatic, soil and anthropogenic drivers affect CH4 fluxes, but it is poorly known the relative weight of each driver and whether all drivers have similar effects across forest biomes. We compiled a database of 478 in situ estimations of CH4 fluxes in forest soils from 191 peer-reviewed studies. All forest biomes (boreal, temperate, tropical and subtropical) but savannahs act on average as CH4 sinks, which presented positive fluxes in 65% of the sites. Mixed effects models showed that combined climatic and edaphic variables had the best support, but anthropogenic factors did not have a significant effect on CH4 fluxes at global scale. This model explained only 19% of the variance in soil CH4 flux which decreased with declines in precipitation and increases in temperature, and with increases in soil organic carbon, bulk density and soil acidification. The effects of these drivers were inconsistent across biomes, increasing the model explanation of observed variance to 34% when the drivers have a different slope for each biome. Despite this limited explanatory value which could be related to the use of soil variables calculated at coarse scale (~1 km), our study shows that soil CH4 fluxes in forests are determined by different environmental variables in different biomes. The most sensitive system to all studied drivers were the temperate forests, while boreal forests were insensitive to climatic variables, but highly sensitive to edaphic factors. Subtropical forests and savannahs responded similarly to climatic variables, but differed in their response to soil factors. Our results suggest that the increase in temperature predicted in the framework of climate change would promote CH4 emission (or reduce CH4 sink) in subtropical and savannah forests, have no influence in boreal and temperate forests and promote uptake in tropical forests.

24 citations


Additional excerpts

  • ...Note: 1—Curry (2007); 2—Liu et al. (2019); 3—Ridgwell et al. (1999); 4—Yu et al. (2017); 5—Aronson et al. (2013); 6—Dijkstra et al. (2012); 7—Dutaur and Verchot (2007); 8—Del Grosso et al. (2000); 9—Weslien et al. (2009); 10—Zhang et al....

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  • ...and landfills (Kirschke et al., 2013). This GHG is mostly consumed in the troposphere through oxidation by hydroxyl (·OH) radicals (90%), whereas only 6% is oxidized by methanotrophs in aerated soils (Kirschke et al., 2013; Le Mer & Roger, 2001). Despite its small proportion, it is a sink that can be directly affected by human interventions through land-use conservation, change or intensification. Soils of forest ecosystems are the most important terrestrial components acting as a sink of atmospheric CH4 (Dutaur & Verchot, 2007). Of the total CH4 consumed in soils at global scale, 60% corresponds to forest ecosystems which uptake 9.16 Tg CH4/year, followed by grasslands with 3.73 Tg CH4/year (Dutaur & Verchot, 2007; Yu, Huang, Zhang, Li, & Sun, 2017). However, declines in soil CH4 uptake has been identified in several forests across the globe, as a consequence of the joint effect of climate change and land-use changes (Han & Zhu, 2020; Ni & Groffman, 2018). Therefore, unravelling the combination of the environmental drivers that determines the CH4 flux in forest soils, both in natural and planted forests, and whether they have a similar behaviour in response to they across biomes, is a crucial step to improve our ability to manage—to some extent—CH4 mitigation and to predict the potential changes of this process under global warming. At soil level, CH4 is produced by methanogenic micro-organism (methanogens) as an end result of the anaerobic digestion of organic matter, but also it is consumed by biological oxidation carried out by methane-oxidizing bacteria (methanotrophs; Le Mer & Roger, 2001). Each of these processes has different environmental requirements, being methanogenesis dominant under anaerobic conditions and methanotrophy active under aerobic conditions (Le Mer & Roger, 2001). Therefore, the net CH4 flux in soils depend on the interplay between aerobic and anaerobic conditions mainly driven by temporal and spatial dynamics of soil water balance (Le Mer & Roger, 2001; Liu, Estiarte, & Peñuelas, 2019; Ni & Groffman, 2018). Furthermore, net negative soil CH4 flux (hereafter soil CH4 uptake) occurs when oxidation process overcomes the methanogenesis (Le Mer & Roger, 2001). Because soil water balance at ecosystem level is controlled by precipitation (water input) and temperature (evaporative output), as well as the vegetation cover, large-scale variations in soil CH4 uptake could be closely linked to climatic variation. However, global scale empirical models considering sole climatic variables have shown to have a limited explicative power (with an explained variance lower than 10%; Dutaur & Verchot, 2007; Liu et al., 2019). In contrast, higher predictive power was reached when soil variables influencing methanotrophy had been added to climatic predictors by Yu et al. (2017). In that study, however, the increase in goodness of fit was achieved by adding complex CH4 flux–soil predictors relationships (i....

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  • ...Note: 1—Curry (2007); 2—Liu et al. (2019); 3—Ridgwell et al. (1999); 4—Yu et al. (2017); 5—Aronson et al. (2013); 6—Dijkstra et al....

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  • ...Note: 1—Curry (2007); 2—Liu et al. (2019); 3—Ridgwell et al. (1999); 4—Yu et al. (2017); 5—Aronson et al. (2013); 6—Dijkstra et al. (2012); 7—Dutaur and Verchot (2007); 8—Del Grosso et al. (2000); 9—Weslien et al. (2009); 10—Zhang et al. (2014); 11—Han and Zhu (2020); 12—Hiltbrunner et al....

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  • ...Note: 1—Curry (2007); 2—Liu et al. (2019); 3—Ridgwell et al. (1999); 4—Yu et al....

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Journal ArticleDOI
TL;DR: The diversity of known MBs as well as the genetics underlying MB biosynthesis are described, and it is proposed based on bioinformatics analyses that some methanotrophs may produce novel forms of MB that have yet to be characterized.
Abstract: Aerobic methane-oxidizing bacteria of the Alphaproteobacteria have been found to express a novel ribosomally synthesized post-translationally modified polypeptide (RiPP) termed methanobactin (MB). The primary function of MB in these microbes appears to be for copper uptake, but MB has been shown to have multiple capabilities, including oxidase, superoxide dismutase and hydrogen peroxide reductase activities, the ability to detoxify mercury species, as well as acting as an antimicrobial agent. Herein, we describe the diversity of known MBs as well as the genetics underlying MB biosynthesis. We further propose based on bioinformatics analyses that some methanotrophs may produce novel forms of MB that have yet to be characterized. We also discuss recent findings documenting that MBs play an important role in controlling copper availability to the broader microbial community, and as a result can strongly affect the activity of microbes that require copper for important enzymatic transformations, e.g. conversion of nitrous oxide to dinitrogen. Finally, we describe procedures for the detection/purification of MB, as well as potential medical and industrial applications of this intriguing RiPP.

21 citations

Journal ArticleDOI
TL;DR: Evidence is provided, using culture-dependent and culture-independent methods, that Methylocella are abundant and active at terrestrial natural gas seeps, suggesting that they play a significant role in the biogeochemical cycling of these gaseous alkanes.
Abstract: Natural gas seeps contribute to global climate change by releasing substantial amounts of the potent greenhouse gas methane and other climate-active gases including ethane and propane to the atmosphere. However, methanotrophs, bacteria capable of utilising methane as the sole source of carbon and energy, play a significant role in reducing the emissions of methane from many environments. Methylocella-like facultative methanotrophs are a unique group of bacteria that grow on other components of natural gas (i.e. ethane and propane) in addition to methane but a little is known about the distribution and activity of Methylocella in the environment. The purposes of this study were to identify bacteria involved in cycling methane emitted from natural gas seeps and, most importantly, to investigate if Methylocella-like facultative methanotrophs were active utilisers of natural gas at seep sites. The community structure of active methane-consuming bacteria in samples from natural gas seeps from Andreiasu Everlasting Fire (Romania) and Pipe Creek (NY, USA) was investigated by DNA stable isotope probing (DNA-SIP) using 13C-labelled methane. The 16S rRNA gene sequences retrieved from DNA-SIP experiments revealed that of various active methanotrophs, Methylocella was the only active methanotrophic genus common to both natural gas seep environments. We also isolated novel facultative methanotrophs, Methylocella sp. PC1 and PC4 from Pipe Creek, able to utilise methane, ethane, propane and various non-gaseous multicarbon compounds. Functional and comparative genomics of these new isolates revealed genomic and physiological divergence from already known methanotrophs, in particular, the absence of mxa genes encoding calcium-containing methanol dehydrogenase. Methylocella sp. PC1 and PC4 had only the soluble methane monooxygenase (sMMO) and lanthanide-dependent methanol dehydrogenase (XoxF). These are the first Alphaproteobacteria methanotrophs discovered with this reduced functional redundancy for C-1 metabolism (i.e. sMMO only and XoxF only). Here, we provide evidence, using culture-dependent and culture-independent methods, that Methylocella are abundant and active at terrestrial natural gas seeps, suggesting that they play a significant role in the biogeochemical cycling of these gaseous alkanes. This might also be significant for the design of biotechnological strategies for controlling natural gas emissions, which are increasing globally due to unconventional exploitation of oil and gas.

20 citations

Journal ArticleDOI
TL;DR: In this paper, the most recent advances in Type II methanotrophs related to multi-omics studies and metabolic engineering are reviewed and representative examples and prospects of metabolic engineering strategies for the production of suitable products are also discussed.

19 citations

References
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Journal ArticleDOI
25 Mar 2010-Nature
TL;DR: Evidence for a fourth pathway to produce oxygen is presented, possibly of considerable geochemical and evolutionary importance, and opens up the possibility that oxygen was available to microbial metabolism before the evolution of oxygenic photosynthesis.
Abstract: Only three biological pathways are known to produce oxygen: photosynthesis, chlorate respiration and the detoxification of reactive oxygen species. Here we present evidence for a fourth pathway, possibly of considerable geochemical and evolutionary importance. The pathway was discovered after metagenomic sequencing of an enrichment culture that couples anaerobic oxidation of methane with the reduction of nitrite to dinitrogen. The complete genome of the dominant bacterium, named ‘Candidatus Methylomirabilis oxyfera’, was assembled. This apparently anaerobic, denitrifying bacterium encoded, transcribed and expressed the well-established aerobic pathway for methane oxidation, whereas it lacked known genes for dinitrogen production. Subsequent isotopic labelling indicated that ‘M. oxyfera’ bypassed the denitrification intermediate nitrous oxide by the conversion of two nitric oxide molecules to dinitrogen and oxygen, which was used to oxidize methane. These results extend our understanding of hydrocarbon degradation under anoxic conditions and explain the biochemical mechanism of a poorly understood freshwater methane sink. Because nitrogen oxides were already present on early Earth, our finding opens up the possibility that oxygen was available to microbial metabolism before the evolution of oxygenic photosynthesis. A previously unknown pathway producing oxygen during anaerobic methane oxidation linked to nitrite and nitrate reduction has been found in microbes isolated from freshwater sediments in Dutch drainage ditches. The complete genome of the bacterium responsible for this reaction has been assembled, and found to contain genes for aerobic methane oxidation. The bacterium reduces nitrite via the recombination of two molecules of nitric oxide into nitrogen and oxygen, bypassing the familiar denitrification intermediate nitrous oxide. This discovery is relevant to nitrogen and methane cycling in the environment and, since nitrogen oxides arose early on Earth, raises the possibility that oxygen was available to microbes before the advent of oxygen-producing photosynthesis. In certain microbes, the anaerobic oxidation of methane can be linked to the reduction of nitrates and nitrites. Here it is shown that this occurs through the intermediate production of oxygen. This brings the number of known biological pathways for oxygen production to four, with implications for our understanding of life on the early Earth.

1,463 citations

Journal ArticleDOI
TL;DR: The organisms were classified into five groups on the basis of morphology, fine structure, and type of resting stage formed (exospores and different types of cysts) and into subgroups on other properties.
Abstract: SUMMARY More than 100 Gram-negative, strictly aerobic, methane-utilizing bacteria were isolated. All used only methane and methanol of the substrates tested for growth. The organisms were classified into five groups on the basis of morphology, fine structure, and type of resting stage formed (exospores and different types of cysts) and into subgroups on other properties. Methods of enrichment, isolation and culture are described.

1,343 citations

01 Jan 1982

903 citations

Journal ArticleDOI
TL;DR: The diversity of chemosynthetic symbionts and their hosts is focused on, and phylogenetic analyses have shown that these associations have evolved on multiple occasions by convergent evolution.
Abstract: Chemosynthetic symbioses occur in a wide range of ocean habitats, from deep-sea vents and cold seeps to whale falls and shallow-water sediments. This Review reveals the diversity and complexity of these symbioses, some of which include multiple symbiotic partners. Chemosynthetic symbioses between bacteria and marine invertebrates were discovered 30 years ago at hydrothermal vents on the Galapagos Rift. Remarkably, it took the discovery of these symbioses in the deep sea for scientists to realize that chemosynthetic symbioses occur worldwide in a wide range of habitats, including cold seeps, whale and wood falls, shallow-water coastal sediments and continental margins. The evolutionary success of these symbioses is evident from the wide range of animal groups that have established associations with chemosynthetic bacteria; at least seven animal phyla are known to host these symbionts. The diversity of the bacterial symbionts is equally high, and phylogenetic analyses have shown that these associations have evolved on multiple occasions by convergent evolution. This Review focuses on the diversity of chemosynthetic symbionts and their hosts, and examines the traits that have resulted in their evolutionary success.

852 citations

Book
01 Jun 1982

817 citations