Abstract
The communities and abundances of methanotrophs and methanogens, along with the oxygen, methane, and total organic carbon (TOC) concentrations, were investigated along a depth gradient in a flooded rice paddy. Broad patterns in vertical profiles of oxygen, methane, TOC, and microbial abundances were similar in the bulk and rhizosphere soils, though methane and TOC concentrations and 16S rRNA gene copies were clearly higher in the rhizosphere soil than in the bulk soil. Oxygen concentrations decreased sharply to below detection limits at 8 mm depth. Pyrosequencing of 16S rRNA genes showed that bacterial and archaeal communities varied according to the oxic, oxic-anoxic, and anoxic zones, indicating that oxygen is a determining factor for the distribution of bacterial and archaeal communities. Aerobic methanotrophs were maximally observed near the oxic-anoxic interface, while methane, TOC, and methanogens were highest in the rhizosphere soil at 30–200 mm depth, suggesting that methane is produced mainly from organic carbon derived from rice plants and is metabolized aerobically. The relative abundances of type I methanotrophs such as Methylococcus, Methylomonas, and Methylocaldum decreased more drastically than those of type II methanotrophs (such as Methylocystis and Methylosinus) with increasing depth. Methanosaeta and Methanoregula were predominant methanogens at all depths, and the relative abundances of Methanosaeta, Methanoregula, and Methanosphaerula, and GOM_Arc_I increased with increasing depth. Based on contrasts between absolute abundances of methanogens and methanotrophs at depths sampled across rhizosphere and bulk soils (especially millimeter-scale slices at the surface), we have identified populations of methanogens (Methanosaeta, Methanoregula, Methanocella, Methanobacterium, and Methanosphaerula), and methanotrophs (Methylosarcina, Methylococcus, Methylosinus, and unclassified Methylocystaceae) that are likely physiologically active in situ.
Highlights
Methane (CH4) is the second most important greenhouse gas in the atmosphere, after carbon dioxide
This interface zone, where aerobic methanotrophy certainly occurred in situ, methane concentration increased steadily with depth to maximum levels of 2.7 and 3.3 μg/g-soil at 60–100mm in the bulk and rhizosphere soils, respectively; methane decreased to approximately 0.4 μg/g-soil at the 400-mm depth in both soils (Figure 1A)
In this study, we investigated the communities of methanotrophs as well as methanogens using parallel 454-pyroseqeuncing along a depth gradient comprising the surface and anaerobic regions, along with the analysis of oxygen, methane, and total organic carbon (TOC) concentrations and methanogenic and methanotrophic abundances, in the bulk and rhizosphere soils of the flooded rice paddy
Summary
Methane (CH4) is the second most important greenhouse gas in the atmosphere, after carbon dioxide. Members of the orders Methanomicrobiales, Methanobacteriales, Methanococcales, Methanosarcinales, and Methanocellales have been identified from rice paddies (Sakai et al, 2009; Ma et al, 2012; Lee et al, 2014; Liu et al, 2015) Anaerobic methanotrophs such as the anaerobic methanotrophic archaea (ANME), “Candidatus Methylomirabilis oxyfera,” and “Candidatus Methanoperedens nitroreducens” have recently been reported as putatively important players in methane oxidation (Ettwig et al, 2010; Biddle et al, 2012; Haroon et al, 2013; Shen et al, 2014), it has been suggested that methane is metabolized mainly by aerobic methanotrophs in rice paddies (Groot et al, 2003; Ma et al, 2010, 2013; Lee et al, 2014). Atypical methanotrophs belonging to the family Methylacidiphilaceae of the phylum Verrucomicrobia were reported to be aerobic (Op den Camp et al, 2009)
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