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FEMS Microbiol Ecol. 2016 Dec;92(12). pii: fiw181. Epub 2016 Aug 24.

Distribution and activity of the anaerobic methanotrophic community in a nitrogen-fertilized Italian paddy soil.

Author information

1
Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands.
2
Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands c.lueke@science.ru.nl.
3
CREA - Council for Agricultural Research and Economics, Rice Research Unit, s.s.11 to Torino km 2.5, 13100 Vercelli, Italy.

Abstract

In order to mitigate methane emissions from paddy fields, it is important to understand the sources and sinks. Most paddy fields are heavily fertilized with nitrite and nitrate, which can be used as electron acceptors by anaerobic methanotrophs. Here we show that slurry incubations of Italian paddy field soil with nitrate and 13C-labelled methane have the potential for nitrate-dependent anaerobic oxidation of methane (79.9 nmol g-1dw d-1). Community analysis based on 16S rRNA amplicon sequencing and qPCR of the water-logged soil and the rhizosphere showed that anaerobic oxidation of methane-associated archaea (AAA), including Methanoperedens nitroreducens, comprised 9% (bulk soil) and 1% (rhizosphere) of all archaeal reads. The NC10 phylum bacteria made up less than 1% of all bacterial sequences. The phylogenetic analysis was complemented by qPCR showing that AAA ranged from 0.28 × 106 to 3.9 × 106 16S rRNA gene copies g-1dw in bulk soil and 0.27 × 106 to 2.8 × 106 in the rhizosphere. The abundance of NC10 phylum bacteria was an order of magnitude lower. Revisiting published diversity studies, we found that AAA have been detected, but not linked to methane oxidation, in several paddy fields. Our data suggest an important role of AAA in methane cycling in paddy fields.

KEYWORDS:

16S rRNA gene; AAA; Methanoperedens nitroreducens; amplicon sequencing; anaerobic oxidation of methane; microbial community; paddy fields; rice rhizosphere

PMID:
27562776
DOI:
10.1093/femsec/fiw181

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