High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy

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.

High‐resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils

“…It is well-known that the combined effects of depthcorrelated geochemical redox gradients (Cadillo-Quiroz et al, 2006;Lazar et al, 2015;Lee et al, 2015;Chu et al, 2016) and water cover (Kotiaho et al, 2010) can be strongly associated with changes in soil microbial communities. However, we also observed OTU-level differences in occupancy and abundance along soil depth gradients, which would not have been predicted based on redox requirements of closely related organisms.…”

“…Unfortunately, many 16S rRNA gene‐based studies employ PCR primers that simultaneously amplify both bacterial and archaeal 16S rRNA genes (Caporaso et al ., ), under‐sampling diversity of the less‐abundant archaeal fraction (Wang et al ., ; Klindworth et al ., ). To more deeply sample the archaeal members, primers specific to this domain have been developed (Baker et al ., ; Teske and Sørensen, ; Klindworth et al ., ), but often produce longer amplicons which have largely limited their use to lower‐throughput sequencing methods such as Sanger sequencing (Gantner et al ., ) and pyrosequencing (Lee et al ., ; Webster et al ., ).…”

Methane flux dynamics in relation to methanogenic and methanotrophic populations in the soil of Indian Sundarban mangroves

“…By contrast, in the surface soil, the average population of methanotrophs was 3.43 times higher than that of methanogens. The results indicate that most of the CH 4 produced by methanogens from the particular soil segment was utilized by methanotrophs in the mangrove ecosystem under study (Lee, Jeong, Kim, Madsen, & Jeon, ). The maximum CH 4 emission rates (6230 ± 1025.6 µM m −2 day −1 ) were recorded from the soil collected at a 60‐cm depth of the LLZ during the post‐monsoon period (Figure ).…”

Molecular detection of Methylotrophs from an Indian landfill site and their potential for biofuel production

“…(Murrell et al, 1998;Chen et al, 2007;Han et al, 2009;Musenze et al, 2016;Lee et al, 2015;Su et al, 2014). In present study we used 16S rDNA based cloning-sequencing and DGGE for identification and diversity analysis of methylotrophs/methanotrophs present in the leachate samples of Ghazipur, Delhi.…”