AUTHOR=Lee Hyo Jung , Jeong Sang Eun , Kim Pil Joo , Madsen Eugene L., Jeon Che Ok 

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

JOURNAL=Frontiers in Microbiology

VOLUME=6

YEAR=2015

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2015.00639

DOI=10.3389/fmicb.2015.00639

ISSN=1664-302X

ABSTRACT=<p>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 <italic>Methylococcus</italic>, <italic>Methylomonas</italic>, and <italic>Methylocaldum</italic> decreased more drastically than those of type II methanotrophs (such as <italic>Methylocystis</italic> and <italic>Methylosinus</italic>) with increasing depth. <italic>Methanosaeta</italic> and <italic>Methanoregula</italic> were predominant methanogens at all depths, and the relative abundances of <italic>Methanosaeta</italic>, <italic>Methanoregula</italic>, and <italic>Methanosphaerula</italic>, 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 (<italic>Methanosaeta</italic>, <italic>Methanoregula</italic>, <italic>Methanocella</italic>, <italic>Methanobacterium</italic>, and <italic>Methanosphaerula</italic>), and methanotrophs (<italic>Methylosarcina, Methylococcus, Methylosinus</italic>, and unclassified <italic>Methylocystaceae</italic>) that are likely physiologically active <italic>in situ</italic>.</p>