The greenhouse effects of methane and nitrous oxide are significantly higher than carbon dioxide, respectively 23 and 296 times, respectively. Carbon dioxide, methane and nitrous oxide distribute in the atmosphere, and lead the earth’s temperature rising. The wetlands account for more than half of greenhouse gas emissions in the atmosphere than that from water bodies. So the wetlands significantly affect the global climate changes.Soil microorganisms play important roles in maintaining ecological functions of the wetlands. Methane-oxidizer can use methane as the sole carbon and energy, and generate the energy for growth during the oxidation of methane to same amount of carbon dioxide. Methane-oxidizer plays an important role not only in methane consuming, but also in carbon, oxygen, nitrogen cycles in the land-water environments. Methane-oxidizer is the key group for controlling the methane emission and involving in the carbon cycle, and play important roles in greenhouse gas methane emission and in the carbon cycle. Ammonia-oxidation is the key and limiting step of the nitrification which is responsible for deep-sea huge library of nitrate formation. Methane and ammonia-oxidizer have similar substrates methane and ammonia to generate energy respectively. Oxidation of methane and ammonium are two different processes catalyzed by completely unrelated microorganisms. Still, the two processes do have many interesting aspects in common. Aerobic methane-oxidizer involving in the process of methane oxidation is as follows: CH₄→CH₃OH→HCHO→ HCOOH→CO₂. Anaerobic oxidation of methane is a microbial process occurring mainly in anoxic marine sediments, and methane is oxidized with sulfate as the terminal electron acceptor. Anaerobic oxidation of methane is considered to be a very important process reducing the emission of the greenhouse gas methane from the ocean into the atmosphere. It is estimated that almost 90% of all the methane that arises from marine sediments is oxidized anaerobically by this process. Aerobic ammoniaoxidizer, the oxidation of ammonia to hydroxylamine, is catalyzed by ammonia mono- oxygenase, subsequently to NO^-₂  catalyzed by hydroxylamine oxidoreductase. Anammox, a new process of anaerobic ammonium oxidation, combines ammonia and nitrite directly into N₂ gas. This reaction is carried out by anammox bacteria belonging to the planctomycete group. The anammox reaction can be represented as NH⁺₄ + NO^-₂=N₂+ 2H₂O .
It is important for understanding the biogeochemical cycle to explore the microbial distribution and community structure and so on. At present, traditional cultivation-dependent methods help us understand the culturable microorganisms. Most microorganisms need molecular ecological methods to detect due to the uncultured. These methods include Phospholipids Fatty Acids, Amplified Ribosomal DNA Restriction Analysis, Restriction Fragment Length Polymorphism, Terminal Restriction Fragment Length Polymorphism, Random Amplification Polymorphism DNA, Single Strand Conformation Polymorphism, Denatured Gradient Gel Electrophoresis, Fluorescent in Situ Hybridization, PLFA-based SIP, DNA-based SIP, RNA-based SIP, Pyro-sequencing, PhyloChip^TM, Geochip^TM and so on. But the traditional methods are still important for researchers to sequence the whole genome of the culturable microorganisms and to deeply explore the similar microorganism group, such as sequencing the genome of Candidatus “Nitrosopumilus maritimus” strain SCM1 and Methylococcus capsulatus.
In this review, we discuss microbial mechanisms of the methaneand ammonia-oxidation processes; normally molecular methods for understanding these functional groups; the roles and significance of methane-oxidizer in the carbon cycle and controlling the greenhouse gas emission; the roles and significance of ammonia-oxidizer in the nitrogen cycle and controlling the greenhouse gas emission. Finally, We illuminate the common scientific problems facing in the methane-and ammonia-oxidizer studies.