N 2 O emissions by nitrifiers are often estimated using selective inhibitors, such as 1‐alkynes. However, the effects of these inhibitors on anaerobic ammonium‐oxidising (anammox) bacteria are largely unknown. In this study, we assessed the inhibitory effect of linear and aromatic alkynes on anammox activity and identified their target enzyme. ‘ Candidatus Kuenenia stuttgartiensis’ biomass and constructed wetland soil samples...

Northern peatlands, ecosystems which store enormous amounts of carbon, and yet are major sources of methane and plant‐derived volatiles including isoprene, are predicted to be greatly affected by climate change. Isoprene, the major volatile secondary metabolite released by plants, can support the carbon and energy needs of a variety of bacteria. Here we show that Sphagnum moss from an acidic bog harboured highly active isopren...

Ammonia‐oxidising archaea (AOA) are important microorganisms contributing towards the nitrogen flux in the environment. Unlike archaea from other major phyla, genetic tools are yet to be developed for the AOA, and identification of antibiotic resistance markers for selecting mutants is required for a genetic system. The aim of this study was to test the effects of selected antibiotics (hygromycin B, neomycin, apramycin, puromy...

The activities of bacterioplankton sustain open ocean biogeochemical and ecological processes, however, little is known about the activity of specific bacterioplankton, especially related to their biogeography across oceanic scales. The Atlantic is the second largest of the world’s oceans and has an essential role in the global carbon cycle. Here, we show congruence in the structure of 16S rRNA and 16S rRNA gene derived bacter...

The ammonia monooxygenase (AMO) is a key enzyme in ammonia‐oxidizing archaea, which are abundant and ubiquitous in soil environments. The AMO belongs to the copper‐containing membrane monooxygenase (CuMMO) enzyme superfamily, which also contains particulate methane monooxygenase (pMMO). Enzymes in the CuMMO superfamily are promiscuous, which results in co‐oxidation of alternative substrates. The phylogenetic and structural sim...

Isoprene (2‐methyl‐1,3‐butadiene) is emitted to the atmosphere each year in sufficient quantities to rival methane (>500 Tg C yr −1 ), primarily due to emission by trees and other plants. Chemical reactions of isoprene with other atmospheric compounds, such as hydroxyl radicals and inorganic nitrogen species (NO x ), have implications for global warming and local air quality, respectively. For many years, it has been estimated...

Bacteria that inhabit soils and the leaves of trees partially mitigate the release of the abundant volatile organic compound, isoprene (2‐methyl‐1,3‐butadiene). While the initial steps of isoprene metabolism were identified in Rhodococcus sp. AD45 two decades ago, the isoprene metabolic pathway still remains largely undefined. Limited understanding of the functions of isoG , isoJ and aldH and uncertainty in the route of isopre...

Summary The Zoige wetland of the Tibetan Plateau is one of the largest alpine wetlands in the world and a major emission source of methane. Methane oxidation by methanotrophs can counteract the global warming effect of methane released in the wetlands. Understanding methanotroph activity, diversity and metabolism at the molecular level can guide the isolation of the uncultured microorganisms and inform strategy‐making decision...

Summary The release of abiotic methane from marine seeps into the atmosphere is a major source of this potent greenhouse gas. Methanotrophic microorganisms in methane seeps use methane as carbon and energy source, thus significantly mitigating global methane emissions. Here, we investigated microbial methane oxidation at the sediment–water interface of a shallow marine methane seep. Metagenomics and metaproteomics, combined wi...

Summary Approximately one‐third of volatile organic compounds (VOCs) emitted to the atmosphere consists of isoprene, originating from the terrestrial and marine biosphere, with a profound effect on atmospheric chemistry. However, isoprene provides an abundant and largely unexplored source of carbon and energy for microbes. The potential for isoprene degradation in marine and estuarine samples from the Colne Estuary, UK, was in...

Summary Nitrogen is a key limiting resource for biomass production in the marine environment. Methylated amines, released from the degradation of osmolytes, could provide a nitrogen source for marine microbes. Thus far, studies in aquatic habitats on the utilization of methylamine, the simplest methylated amine, have mainly focussed on the fate of the carbon from this compound. Various groups of methylotrophs, microorganisms t...

Summary The volatile organosulfur compound, dimethylsulfide (DMS), plays an important role in climate regulation and global sulfur biogeochemical cycles. Microbial oxidation of DMS to dimethylsulfoxide (DMSO) represents a major sink of DMS in surface seawater, yet the underlying molecular mechanisms and key microbial taxa involved are not known. Here, we reveal that Ruegeria pomeroyi , a model marine heterotrophic bacterium, c...

Summary Emissions of biogenic volatile organic compounds (bVOCs), are an important element in the global carbon cycle, accounting for a significant proportion of fixed carbon. They contribute directly and indirectly to global warming and climate change and have a major effect on atmospheric chemistry. Plants emit isoprene to the atmosphere in similar quantities to emissions of methane from all sources and each accounts for app...

Summary Choline is ubiquitous in marine eukaryotes and appears to be widely distributed in surface marine waters; however, its metabolism by marine bacteria is poorly understood. Here, using comparative genomics and molecular genetic approaches, we reveal that the capacity for choline catabolism is widespread in marine heterotrophs of the marine Roseobacter clade ( MRC ). Using the model bacterium R uegeria pomeroyi , we confi...

Summary The xox F gene, encoding a pyrroloquinoline quinone‐dependent methanol dehydrogenase, is found in all known proteobacterial methylotrophs. In several newly discovered methylotrophs, XoxF is the active methanol dehydrogenase, catalysing the oxidation of methanol to formaldehyde. Apart from that, its potential role in methylotrophy and carbon cycling is unknown. So far, the diversity of xox F in the environment has recei...

Summary A variety of culture‐independent techniques have been developed that can be used in conjunction with culture‐dependent physiological and metabolic studies of key microbial organisms in order to better understand how the activity of natural populations influences and regulates all major biogeochemical cycles. In this study, we combined deoxyribonucleic acid‐stable isotope probing (DNA‐SIP) with metagenomics and metaprot...

Summary Emissions of biogenic volatile organic compounds ( VOCs ) form an important part of the global carbon cycle, comprising a significant proportion of net ecosystem productivity. They impact atmospheric chemistry and contribute directly and indirectly to greenhouse gases. Isoprene, emitted largely from plants, comprises one third of total VOCs , yet in contrast to methane, which is released in similar quantities, we know...

Summary Biological oxidation of methane to methanol by aerobic bacteria is catalysed by two different enzymes, the cytoplasmic or soluble methane monooxygenase ( sMMO ) and the membrane‐bound or particulate methane monooxygenase ( pMMO ). Expression of MMOs is controlled by a ‘copper‐switch’, i.e. sMMO is only expressed at very low copper : biomass ratios, while pMMO expression increases as this ratio increases. Methanotrophs...

Summary Methane is an important greenhouse gas and microbes in the environment play major roles in both global methane emissions and terrestrial sinks. However, a full mechanistic understanding of the response of the methane cycle to global change is lacking. Recent studies suggest that a number of biological and environmental processes can influence the net flux of methane from soils to the atmosphere but the magnitude and di...

Summary To determine whether the diversity of phenanthrene‐degrading bacteria in an aged polycyclic aromatic hydrocarbon (PAH) contaminated soil is affected by the addition of plant root exudates, DNA stable isotope probing (SIP) was used. Microcosms of soil with and without addition of ryegrass exudates and with 13 C‐labelled phenanthrene (PHE) were monitored over 12 days. PHE degradation was slightly delayed in the presence...

Summary A new pathway of dimethylsulfide (DMS) metabolism was identified in a novel species of Gammaproteobacteria , Methylophaga thiooxidans sp. nov., in which tetrathionate (S 4 O 6 2− ) was the end‐product of DMS oxidation. Inhibitor evidence indicated that DMS degradation was initiated by demethylation, catalysed by a corrinoid demethylase. Thiosulfate was an intermediate, which was oxidized to tetrathionate by a cytochrom...

Summary Peatlands represent an enormous carbon reservoir and have a potential impact on the global climate because of the active methanogenesis and methanotrophy in these soils. Uncultivated methanotrophs from seven European peatlands were studied using a combination of molecular methods. Screening for methanotroph diversity using a particulate methane monooxygenase‐based diagnostic gene array revealed that Methylocystis ‐rela...

Summary The concentrations of one‐carbon substrates that fuel methylotrophic microbial communities in the ocean are limited and the specialized guilds of bacteria that use these molecules may exist at low relative abundance. As a result, these organisms are difficult to identify and are often missed with existing cultivation and gene retrieval methods. Here, we demonstrate a novel proof of concept: using environmentally‐releva...

Summary The active methanotroph community was investigated for the first time in heather ( Calluna )‐covered moorlands and Sphagnum / Eriophorum ‐covered UK peatlands. Direct extraction of mRNA from these soils facilitated detection of expression of methane monooxygenase genes, which revealed that particulate methane monooxygenase and not soluble methane monooxygenase was probably responsible for CH 4 oxidation in situ , becau...