**3. The microbiota involved in the cycling of CH4**

The amount of CH4 emitted from an ecosystem is the result of the balance between the production of CH4 (methanogenesis) and the consumption (oxidation) of this gas (methanotrophy). Therefore, the emission of CH4 into the atmosphere is determined by activity of methanogenic and methanotrophic microorganisms.

Methanogenic *Archaea* are widely ubiquitous in nature and have been detected in a wide range of environments, including freshwater sediments, hypersaline and rice lakes, anaerobic digesters, permafrost, and landfills, among others. They have a unique enzyme designed methyl-coenzyme M reductase (Mcr), which makes them specialized in producing CH4 [39]. This group of microorganisms presents high diversity in morphology and physiological parameters [40].

The methanogenic microorganisms belong to the *Euryarchaeota* phylum and until recently were classified into seven orders (*Methanobacteriales, Methanococcales, Methanomicrobiales, Methanosarcinales, Methanocellales, Methanopyrales*, and *Methanomassiliicoccales*). The discovery of the genes involved in methanogenesis in *Bathyarchaeota* and subsequently *Verstraetearchaeota* led to a paradigm shift, demonstrating that the evolutionary origin of methanogenesis is prior to the phylum *Euryarchaeota* [41].

The metabolism of methanogenic *Archaea* gains energy by reducing C compounds (e.g., CO2, formate, acetate, methanol, ethanol, methylamines, and methyl sulfides) to CH4 [23]. Thus, traditional methanogenic strains are widely characterized as hydrogenotrophic, acetoclastic, and methylotrophic based on the use of substrate. In most cases, the methane-producing pathways in the environment are determined by DNA sequencing of the corresponding methanogenic microorganisms [39]. The final step in all of these pathways is common and involves the conversion of methyl-S-CoM into CH4 by methyl-coenzyme M reductase (Mcr) [42].

Taking into consideration the production pathway (**Figure 1**), hydrogenotrophic methanogenic microorganisms are known as H2 oxidant, formate, or some simple alcohols and reduce CO2 to CH4 [43]. Most of the described methanogenic microorganisms are hydrogenotrophic. Acetoclastic methanogens divide acetate to form CH4 and CO2. They are found in habitats where hydrogenotrophic methanogenic microorganisms reduce H2 levels sufficiently to create the necessary conditions for the formation of high levels of acetate. Methylotrophic methanogenic microorganisms are common in sulfate-rich marine and hypersaline sediments, in which they use methylated compounds such as trimethylamine, dimethyl sulfate, and methanol [44]. In contrast, in sediments from freshwater environments, it is believed so far that methylotrophic methanogenesis is of little importance, although this is not what recent unpublished results have revealed for the floodable areas of the Amazon. However, the same reasoning used for anaerobic methanotrophy may be occurring in this case.

Methyl compounds, especially methanol, may play an underestimated role as contributors to the production of CH4 in wetlands [44]. Although the use of methanol in the presence of hydrogen has been observed among methanogenic *Archaea*,

*Methane, Microbes and Models in Amazonian Floodplains: State of the Art and Perspectives DOI: http://dx.doi.org/10.5772/intechopen.90247*

#### **Figure 1.**

*Conceptual illustration of CH4 production and consumption prior to atmospheric release in wetland ecosystems. Microorganisms degrade complex organic material in anoxic system by a multistep process, leading to CO2 and CH4 as end products. Adapted from [34].*

this substrate is rarely tested during the description of new species. This lack of information represents a serious obstacle to the analysis of metabolic abilities of methanogenic *Archaea* [45].

Meyer et al. [46] used a metagenomic approach to assess the relative abundance of genes involved in cycling CH4 in forest and pasture soils in Western Amazon and they revealed that genes involved in methanogenesis from methylated compounds were significantly more abundant in the pasture. Soil methylotrophs call attention to the central role of these organisms in global methanol conversions, which mainly originate from plants [47] released from both living and decomposing plant material [48]. Soil microbiota is an essential component of plant decomposition and formation of organic matter. Thus, the understanding about these communities, as well as the one regarding decomposed material, is essential to elucidate the dynamics of these environments.

The literature mentions that in tropical alluvial plains the predominant microbial pathways in methane production are acetoclastic and hydrogenotrophic [49, 50]. However, Alves [51], when evaluating the enrichment of primary and secondary forest and pasture samples in the Amazon, indicated a higher production of CH4 by acetoclastic and methylotrophic pathways.

In flooded areas, known to have high methanogenic rates, methanotrophs are responsible for catalyzing the oxidation of CH4 at the aerobic-anaerobic interfaces. Methanotrophic bacteria are able to use CH4 as their sole source of C [52] and can be divided into four groups: Gammaproteobacteria (often referred as Type I or Type X); Alphaproteobacteria (formerly known as Type II); Verrucomicrobia; and NC10 phylum members [53].

Methanotrophic activity is only viable because of an enzyme known as monooxygenase methane (MMO), which acts in two distinct forms: particulate (pMMO), within an intracellular membrane, or soluble (sMMO), in the cytoplasm. Both convert CH4 into the readily assimilated product, methanol [54].

The oxidations of CH4 have proven to be an important sink for this gas produced by sediments in the Amazon, reducing the amount of CH4 that reaches the atmosphere [8, 55].

The diversity of CH4 metabolizers or metabolizing organisms tends to increase in the near future due to additional findings in surveys using a metagenomic approach and other increasingly robust approaches to the study of microbial diversity. This can be the currently ambiguous evolutionary history of this important metabolic function [23].
