Methane (CH₄) is produced in many natural systems that are vulnerable to change under a warming climate, yet current CH₄ budgets, as well as future shifts in CH₄ emissions, have high uncertainties. Climate change has the potential to increase CH₄ emissions from critical systems such as wetlands, marine and freshwater systems, permafrost, and methane hydrates, through shifts in temperature, hydrology, vegetation, landscape disturbance, and sea level rise. Increased CH₄ emissions from these systems would in turn induce further climate change, resulting in a positive climate feedback. Here we synthesize biological, geochemical, and physically focused CH₄ climate feedback literature, bringing together the key findings of these disciplines. We discuss environment‐specific feedback processes, including the microbial, physical, and geochemical interlinkages and the timescales on which they operate, and present the current state of knowledge of CH₄ climate feedbacks in the immediate and distant future. The important linkages between microbial activity and climate warming are discussed with the aim to better constrain the sensitivity of the CH₄ cycle to future climate predictions. We determine that wetlands will form the majority of the CH₄ climate feedback up to 2100. Beyond this timescale, CH₄ emissions from marine and freshwater systems and permafrost environments could become more important. Significant CH₄ emissions to the atmosphere from the dissociation of methane hydrates are not expected in the near future. Our key findings highlight the importance of quantifying whether CH₄ consumption can counterbalance CH₄ production under future climate scenarios.

Summary: Anaerobic ammonium‐oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the ‘ Candidatus Scalindua’ species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by ‘ Candidatus Scalindua profunda’ to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater ‘ Candidatus Kuenenia stuttgartiensis’. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K. stuttgartiensis could not be found in S. profunda . Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm.

The microbes in the gastrointestinal (GI) tract are of high importance for the health of the host. In this study, Roche 454 pyrosequencing was applied to a pooled set of different 16S rRNA gene amplicons obtained from GI content of common carp (Cyprinus carpio) to make an inventory of the diversity of the microbiota in the GI tract. Compared to other studies, our culture-independent investigation reveals an impressive diversity of the microbial flora of the carp GI tract. The major group of obtained sequences belonged to the phylum Fusobacteria. Bacteroidetes, Planctomycetes and Gammaproteobacteria were other well represented groups of micro-organisms. Verrucomicrobiae, Clostridia and Bacilli (the latter two belonging to the phylum Firmicutes) had fewer representatives among the analyzed sequences. Many of these bacteria might be of high physiological relevance for carp as these groups have been implicated in vitamin production, nitrogen cycling and (cellulose) fermentation.

The present day wastewater treatment practise can be significantly improved when new microbial processes are introduced. In this paper a new concept is discussed along general lines. The concept consists of a first stage in which a maximal sludge production is achieved. In this way COD is removed as sludge and aeration requirements minimized. This sludge can be digested to yield methane for energy generation. The nitrogen removal is based on a partial oxidation to nitrite and subsequent denitrification with ammonium as electron donor.