Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications

Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy

Plastic photodegradation under simulated marine conditions

Ocean plastic pollution is a problem of increasing magnitude; yet, the amount of plastic at the sea surface is much lower than expected. Solar ultraviolet (UV) radiation can induce photodegradation, but its importance in determining the longevity of floating plastic remains unconstrained. Here, we measured photodegradation rates of different plastic types slightly larger than microplastics (virgin polymers and floating plastic debris) under simulated marine conditions. UV irradiation caused all plastic types to leach dissolved organic carbon, and to a lesser degree carbon dioxide, carbon monoxide, methane, and other hydrocarbon gases. The release of photodegradation products translates to degradation rates of 1.7–2.3 % yr−1 of the tested plastic particles normalized to conditions as found in the subtropical surface ocean. Modelling the accumulation of floating plastic debris, our results show that solar UV radiation could already have degraded 7 to 22 % of all floating plastic that has ever been released to the sea

Plastic photodegradation under simulated marine conditions

Ocean plastic pollution is a problem of increasing magnitude; yet, the amount of plastic at the sea surface is much lower than expected. Solar ultraviolet (UV) radiation can induce photodegradation, but its importance in determining the longevity of floating plastic remains unconstrained. Here, we measured photodegradation rates of different plastic types slightly larger than microplastics (virgin polymers and floating plastic debris) under simulated marine conditions. UV irradiation caused all plastic types to leach dissolved organic carbon, and to a lesser degree carbon dioxide, carbon monoxide, methane, and other hydrocarbon gases. The release of photodegradation products translates to degradation rates of 1.7–2.3 % yr−1 of the tested plastic particles normalized to conditions as found in the subtropical surface ocean. Modelling the accumulation of floating plastic debris, our results show that solar UV radiation could already have degraded 7 to 22 % of all floating plastic that has ever been released to the sea

Supplementary data

For nanoSIMS measurements of R. mucilaginosa cells, we analyzed three sample sets: (i) the original inoculum (Control), (ii) after incubation with 13C-labelled polyethylene without and (iii) with UV-treatment. We measured a total of 1144 regions of interest (ROIs, i.e., corresponding to 1144 individual cells). For IRMS and GCMS measurements we measured 3 replicates for the development of ?13C-CO2 values and CO2 concentration in incubations with R. mucilaginosa (RM) and with 13C-polyethylene (PE), with prior UV-treatment (+UV) and without (-UV) as the sole carbon source as well as in incubations with UV-treated 13C-polyethylene (PE) without R. mucilaginosa

Supplementary data

NanoSIMS measurements of R. mucilaginosa cells, where we analyzed three sample sets: (i) the original inoculum, (ii) after incubation with 13C-labelled polyethylene without and (iii) with UV-treatment. We measured a total of 1144 regions of interest (ROIs, i.e., corresponding to 1144 individual cells) Development of ?13C-CO2 values in incubations with R. mucilaginosa (RM) and with 13C-polyethylene (PE), with prior UV-treatment (+UV) and without (-UV) as the sole carbon source as well as in incubations without R. mucilaginosa

Stratification of Diversity and Activity of Methanogenic and Methanotrophic Microorganisms in a Nitrogen-Fertilized Italian Paddy Soil

Contains fulltext : 179231.pdf (publisher's version ) (Open Access)Paddy fields are important ecosystems, as rice is the primary food source for about half of the world’s population. Paddy fields are impacted by nitrogen fertilization and are a major anthropogenic source of methane. Microbial diversity and methane metabolism were investigated in the upper 60cm of a paddy soil by qPCR, 16S rRNA gene amplicon sequencing and anoxic 13C-CH4 turnover with a suite of electron acceptors. The bacterial community consisted mainly of Acidobacteria, Chloroflexi, Proteobacteria, Planctomycetes and Actinobacteria. Among archaea, Euryarchaeota and Bathyarchaeota dominated over Thaumarchaeota in the upper 30cm of the soil. Bathyarchaeota constituted up to 45% of the total archaeal reads in the top 5cm. In the methanogenic community, Methanosaeta were generally more abundant than the versatile Methanosarcina. The measured maximum methane production rate was 444 nmol gdwh-1, and the maximum rates of nitrate-, nitrite- and iron-dependent anaerobic oxidation of methane (AOM) were 57 nmol, 55 nmol and 56 nmol gdwh-1, respectively, at different depths. qPCR revealed a higher abundance of ‘Candidatus Methanoperedens nitroreducens’ than methanotrophic NC10 phylum bacteria at all depths, except at 60cm. These results demonstrate that there is substantial potential for anaerobic oxidation of methane in fertilized paddy fields, with ‘Candidatus Methanoperedens nitroreducens’ archaea as a potential important contributor.15 p

McrA primers for the detection and quantification of the anaerobic archaeal methanotroph ‘Candidatus Methanoperedens nitroreducens’

The nitrogen and methane cycles are important biogeochemical processes. Recently, ‘Candidatus Methanoperedens nitroreducens,’ archaea that catalyze nitrate-dependent anaerobic oxidation of methane (AOM), were enriched, and their genomes were analyzed. Diagnostic molecular tools for the sensitive detection of ‘Candidatus M. nitroreducens’ are not yet available. Here, we report the design of two novel mcrA primer combinations that specifically target the alpha sub-unit of the methyl-coenzyme M reductase (mcrA) gene of ‘Candidatus M. nitroreducens’. The first primer pair produces a fragment of 186-bp that can be used to quantify ‘Candidatus M. nitroreducens’ cells, whereas the second primer pair yields an 1191-bp amplicon that is with sufficient length and well suited for more detailed phylogenetic analyses. Six different environmental samples were evaluated with the new qPCR primer pair, and the abundances were compared with those determined using primers for the 16S rRNA gene. The qPCR results indicated that the number of copies of the ‘Candidatus M. nitroreducens’ mcrA gene was highest in rice field soil, with 5.6 ± 0.8 × 106 copies g−1 wet weight, whereas Indonesian river sediment had only 4.6 ± 2.7 × 102 copies g−1 wet weight. In addition to freshwater environments, sequences were also detected in marine sediment of the North Sea, which contained approximately 2.5 ± 0.7 × 104 copies g−1 wet weight. Phylogenetic analysis revealed that the amplified 1191-bp mcrA gene sequences from the different environments all clustered together with available genome sequences of mcrA from known ‘Candidatus M. nitroreducens’ archaea. Taken together, these results demonstrate the validity and utility of the new primers for the quantitative and sensitive detection of the mcrA gene sequences of these important nitrate-dependent AOM archaea. Furthermore, the newly obtained mcrA sequences will contribute to greater phylogenetic resolution of ‘Candidatus M. nitroreducens’ sequences, which have been only poorly captured by general methanogenic mcrA primers.BT/Environmental Biotechnolog

Effect of water management on microbial diversity and composition in an Italian rice field system

Traditional rice cultivation consumes up to 2500 L of water per kg yield and new strategies such as the 'Alternate Wetting and Drying' (AWD) might be promising water-saving alternatives. However, they might have large impacts on the soil microbiology. In this study, we compared the bacterial and archaeal communities in experimental field plots, cultivated under continuously flooding (CF) and AWD management, by high-throughput sequencing of the 16S rRNA gene. We analysed alpha and beta diversity in bulk soil and on plant roots, in plots cultivated with two different rice cultivars. The strongest difference was found between soil and root communities. Beside others, the anaerobic methanotroph Methanoperedens was abundant in soil, however, we detected a considerable number of ANME-2a-2b on plant roots. Furthermore, root communities were significantly affected by the water management: Differential abundance analysis revealed the enrichment of aerobic and potentially plant-growth-promoting bacteria under AWD treatment, such as Sphingomonadaceae and Rhizobiaceae (both Alphaproteobacteria), and Bacteroidetes families. Microorganisms with an overall anaerobic lifestyle, such as various Delta- and Epsilonproteobacteria, and Firmicutes were depleted. Our study indicates that the bulk soil communities seem overall well adapted and more resistant to changes in the water treatment, whereas the root microbiota seems more vulnerable