Microbial activity in the soil of wetlands is responsible for the emission of more methane (CH4) to the atmosphere than all other natural sources combined (Ciais et al. 2013). This flux is influenced by many factors, but in all cases, the generation of CH4 (methanogenesis) and any oxidation of CH4 (methanotrophy), which may attenuate emissions, are microbially mediated. Therefore, when factors like temperature are cited as influencing wetland CH4 emissions (e.g., Hargreaves and Fowler 1998) they do so by impacting the microbial community either directly (e.g., microbial metabolic rates increase at warmer temperatures), or indirectly by altering other environmental factors, such as plants, which in turn affect the microbial ecosystem (Gill et al. 2017).
The microbial ecosystem inhabiting wetland soils is comprised of a complex mixture of bacteria and archaea that respond to a host of environmental variables. Community composition can vary greatly based on depth in the soil column (Lipson et al. 2013; Bai et al. 2018), geographic setting of the wetland (Grodnitskaya et al. 2018), and types of plants growing in the wetland (Robroek et al. 2015). The majority of microbial species present in wetland soil samples, as in most environments, are uncultured (Ivanova et al. 2016).
Plants impact the wetland microbial community through two primary modes. First, plants exude carbon compounds from their roots which may be more biodegradable than the other soil carbon (Bais et al. 2006; Girkin et al. 2018). These root exudates can stimulate microbial activity and CH4 emissions (Ström et al. 2003; Ström and Christensen 2007; Picek et al. 2007; Chanton et al. 2008; Kayranli et al. 2009). While this increase in CH4 emissions is partially driven by the carbon in the exudates being processed into CH4, the exudates also result in more soil carbon being converted to CH4 (Waldo et al. 2019). This phenomenon is known as the microbial priming effect (Fontaine et al. 2007; Kuzyakov 2010; Ruirui et al. 2014; Ye et al. 2015). The plant growth cycle is seasonal, so changes in root exudation over the plants’ life cycle impacts CH4 emissions even when factors such as temperature are kept constant (Neue et al. 1997).
The second effect that wetland plants have on the microbial environment is leakage of oxygen into the soil from aerenchyma in their roots (Fritz et al. 2011). This oxygen can be used for methanotrophy (Fritz et al. 2011), but other aerobic metabolisms will compete for the limited oxygen supply (Lenzewski et al. 2018). Even when oxygen is used quickly enough that it does not accumulate in the soil (Waldo et al. 2019; Turner et al. 2020), it can influence microbial communities by facilitating the recycling of alternate electron acceptors (Keiluweit et al. 2016), or by creating mixed-redox environments where carbon compounds are partially respired aerobically and partially anaerobically (Chanton et al. 2008). This variety of uses can lead to intense competition for oxygen in the rhizosphere. As with root exudation, oxygen transport changes over time as plants grow throughout the season, and different species of plants allow for varying amounts of oxygen transport (Schimel 1995). The balance between the dynamic effects of root exudation and oxygen transport will control what types of microbial CH4 metabolisms are favored.
In addition to the traditional model of aerobic obligate methanotrophs, the rhizosphere also supports two other methanotrophic metabolisms. Once considered insignificant in wetlands (Conrad 2009), recent work has shown that anaerobic oxidation of CH4 (AOM) is common in freshwater wetlands (Segarra et al. 2015). Though it may be common, AOM is performed by a limited number of microbes, primarily the ANME2d anaerobic archaea (Haroon et al. 2013) and bacteria of the NC10 phylum (He et al. 2016). To avoid the use of oxygen, AOM relies on alternative terminal electron acceptors (TEAs). In freshwater bogs, rain is the primary source of water and nutrients; groundwater is not available to transport TEAs into the wetland. The continued availability of non-oxygen TEAs without transport into bogs can be explained by recycling and regeneration of the TEAs within the wetland (Keller and Bridgham 2007). This recycling requires an ultimate electron sink that is used to regenerate the TEAs used by anaerobic methanotrophs. Plants can supply that electron sink by leaking oxygen from their roots which is used to generate a variety of TEAs in the relatively oxidized rhizosphere (Keiluweit et al. 2016).
The second non-traditional methanotrophic metabolism within the rhizosphere is facultative methanotrophy. Most methanotrophs are only capable of using single-carbon compounds (Conrad 2009). However, some facultative methanotrophs have been found in the genera Methylocella, Methylocapsa, and Methylocystis that can also use carbon compounds such as acetate and ethanol (Dedysh et al. 2005; Dunfield et al. 2010; Belova et al. 2011; Im et al. 2011; Leng et al. 2015). These facultative methanotrophs are widely distributed in the environment, but are especially prevalent in acidic soils, including peatlands (Rahman et al. 2011). Because the rhizosphere is a dynamic soil zone where the balance of microbial activity, root exudation, and oxygen availability may change over time, the ability to use different carbon sources for energy could be a competitive advantage.
Plants have great potential to influence the environment for microbes, including both methanogens and methanotrophs. By doing so, plants impact the amount of CH4, a potent greenhouse gas, which is emitted from wetlands. However, plant effects are not uniform and can either increase (Shannon and White 1994; Joabsson et al. 1999; Popp et al. 2000; Whalen 2005) or decrease (Schipper and Reddy 1996; Fritz et al. 2011; Lenzewski et al. 2018) CH4 emissions. Decreases driven by plants are due to increased methanotrophy (Schipper and Reddy 1996; Fritz et al. 2011; Lenzewski et al. 2018), while increases in CH4 emission can be due to plant-exudate stimulation of CH4 production (Chanton et al. 2008; Waldo et al. 2019; Turner et al. 2020) and/or increased transport through aerenchyma (Shannon and White 1994; Joabsson et al. 1999). Determining metabolisms fostered by the presence of roots can be used to build a mechanistic understanding of why some plant species increase while other decrease CH4 emissions. In this study, we focused on Carex aquatilis, a common wetland sedge shown to increase methane emissions (Schimel 1995; Waldo et al. 2019). We compared the microbial communities of planted and unplanted wetland soil to elucidate how Carex growth influenced populations of methanogens and methanotrophs, with special focus on the different forms of methanotrophy.