1,721,249 research outputs found
Bernard Jouve, Christian Lefèvre (dir.) Horizons métropolitains, Collection Recherche Urbaine, 2004
No full textDumont Marc. Bernard Jouve, Christian Lefèvre (dir.) Horizons métropolitains, Collection Recherche Urbaine, 2004. In: Les Annales de la recherche urbaine, N°97, 2004. Renouvellements urbains. pp. 154-155
Physiology of atmospheric methane-oxidizing bacteria
No full textThe biological sink for atmospheric methane consists of atmospheric methane-oxidizing bacteria (atmMOB) that persistently oxidize atmospheric methane as carbon and energy source and conventional methanotrophs that transiently oxidize atmospheric methane after exposure to elevated methane concentrations. The ecology and environmental activity of atmMOB have been studied for several decades, but until the first detailed characterization in 2019 of an atmMOB in pure culture that can grow with air as the sole energy (methane, carbon monoxide and molecular hydrogen) and carbon (methane and carbon dioxide) source, their physiology was mostly unexplored. Here we summarize the available knowledge about atmMOB physiology, including the kinetics of atmospheric methane oxidation, energy yields during growth on methane and other trace gases from air, carbon assimilation and physiological diversity. We use this background to identify knowledge gaps that should be targeted to support future research on atmMOB.<br/
Identification of active aerobic methanotrophs in plateau wetlands using DNA stable isotope probing
No full textSedge-dominated wetlands on the Qinghai–Tibetan Plateau are methane emission centers. Methanotrophs at these sites play a role in reducing methane emissions, but relatively little is known about the composition of active methanotrophs in these wetlands. Here, we used DNA stable isotope probing to identify the key active aerobic methanotrophs in three sedge-dominated wetlands on the plateau. We found that Methylocystis species were active in two peatlands, Hongyuan and Dangxiong. Methylobacter species were found to be active only in Dangxiong peat. Hongyuan peat had the highest methane oxidation rate, and cross-feeding of carbon from methanotrophs to methylotrophic Hyphomicrobium species was observed. Owing to a low methane oxidation rate during the incubation, the labeling of methanotrophs in Maduo wetland samples was not detected. Our results indicate that there are large differences in the activity of methanotrophs in the wetlands of this region
Stable isotope probing - linking microbial identity to function
No full textStable isotope probing (SIP) is a technique that is used to identify the microorganisms in environmental samples that use a particular growth substrate. The method relies on the incorporation of a substrate that is highly enriched in a stable isotope, such as C-13, and the identification of active microorganisms by the selective recovery and analysis of isotope-enriched cellular components. DNA and rRNA are the most informative taxonomic biomarkers and C-13-labelled molecules can be purified from unlabelled nucleic acid by density-gradient centrifugation. The future holds great promise for SIP, particularly when combined with other emerging technologies such as microarrays and metagenomics
Ammonia oxidation coupled to CO2 fixation by Archaea and Bacteria in an agricultural soil
No full textAmmonia oxidation is an essential part of the global nitrogen cycling and was long thought to be driven only by bacteria. Recent findings expanded this pathway also to the archaea. However, most questions concerning the metabolism of ammonia-oxidizing archaea, such as ammonia oxidation and potential CO2 fixation, remain open, especially for terrestrial environments. Here, we investigated the activity of ammonia-oxidizing archaea and bacteria in an agricultural soil by comparison of RNA- and DNA-stable isotope probing (SIP). RNA-SIP demonstrated a highly dynamic and diverse community involved in CO2 fixation and carbon assimilation coupled to ammonia oxidation. DNA-SIP showed growth of the ammonia-oxidizing bacteria but not of archaea. Furthermore, the analysis of labeled RNA found transcripts of the archaeal acetyl-CoA/propionyl-CoA carboxylase (accA/pccB) to be expressed and labeled. These findings strongly suggest that ammonia-oxidizing archaeal groups in soil autotrophically fix CO2 using the 3-hydroxypropionate–4-hydroxybutyrate cycle, one of the two pathways recently identified for CO2 fixation in Crenarchaeota. Catalyzed reporter deposition (CARD)-FISH targeting the gene encoding subunit A of ammonia monooxygenase (amoA) mRNA and 16S rRNA of archaea also revealed ammonia-oxidizing archaea to be numerically relevant among the archaea in this soil. Our results demonstrate a diverse and dynamic contribution of ammonia-oxidizing archaea in soil to nitrification and CO2 assimilation and that their importance to the overall archaeal community might be larger than previously thought
Assimilation of acetate by the putative atmospheric methane oxidizers belonging to the USCα clade
No full textForest soils are a major biological sink for atmospheric methane, yet the identity and physiology of the microorganisms responsible for this process remain unclear. Although members of the upland soil cluster ? (USC?) are assumed to represent methanotrophic bacteria adapted to the oxidation of the trace level of methane in the atmosphere and to be an important sink of this greenhouse gas, so far they have resisted isolation. In particular, the question of whether the atmospheric methane oxidizers are able to obtain all their energy and carbon solely from atmospheric methane still waits to be answered. In this study, we performed stable-isotope probing (SIP) of RNA and DNA to investigate the assimilation of (13) C-methane and (13) C-acetate by USC? in an acidic forest soil. RNA-SIP showed that pmoA mRNA of USC? was not labelled by (13) C of supplemented (13) C methane, although catalysed reporter deposition - fluorescence in situ hybridization (CARD-FISH) targeting pmoA mRNA of USC? detected its expression in the incubated soil. In contrast, incorporation of (13) C-acetate into USC?pmoA mRNA was observed. USC?pmoA genes were not labelled, indicating that they had not grown during the incubation. Our results indicate that the contribution of alternative carbon sources, such as acetate, to the metabolism of the putative atmospheric methane oxidizers in upland forest soils might be substantial
Dataset for thesis: 'The Interaction between Plants and Rhizosphere Microbes
No full textResearch data supports: Cai, P. (2025). The interaction between plants and Rhizosphere microbes. [Doctoral Thesis, University of Southampton]. , 240pp. his dataset contains:all experimental data used for generating the figures in the thesis, and the zip files are labelled separately according to the figures related. The cvs files are viewable in Microsoft Excel. The data come from DNA sequencing as well as measurement of plant growth promoting traits of bacteria.
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Primers: functional marker genes for methylotrophs and methanotrophs
No full textMethylotrophs are a diverse group of microorganisms that use compounds without a carbon–carbon bond as a sole source of carbon and energy for growth. Methylotrophs play an important role in most environments, including terrestrial, aquatic, and marine habitats. Several approaches to detect and identify methylotrophs in environmental samples have been developed. A common approach is to target protein-encoding genes since methylotrophs are phylogenetically diverse, making the design of 16S rRNA primers and probes with wide coverage difficult or impossible. The mxaF gene encoding the active subunit of the methanol dehydrogenase is one of the more universal targets for methylotrophs, as are some of the genes involved in C1-transfer reactions, such as fhcD gene of methanopterin-linked pathway. The pmoA gene, encoding the beta-subunit of the particulate methane monooxygenase, is a common target for methanotrophs. In many cases the evolution of these functional genes is congruent with the 16S rRNA and other phylogenetic markers, making them suitable for inferring taxonomy. This chapter summarizes the available primers and methods to detect or quantify various aerobic methylotrophs in environmental samples
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