Activity and abundance of methane-oxidizing bacteria in secondary forest and manioc plantations of Amazonian Dark Earth and their adjacent soils

Abstract

The oxidation of atmospheric CH4 in upland soils is mostly mediated by uncultivated groups of microorganisms that have been identified solely by molecular markers, such as the sequence of the pmoA gene encoding the β-subunit of the particulate methane monooxygenase enzyme. The objective of this work was to compare the activity and diversity of methanotrophs in Amazonian Dark Earth soil (ADE, Hortic Anthrosol) and their adjacent non-anthropic soil. Secondly, the effect of land use in the form of manioc cultivation was examined by comparing secondary forest and plantation soils. CH4 oxidation potentials were measured and the structure of the methanotroph communities assessed by quantitative PCR (qPCR) and amplicon pyrosequencing of pmoA genes. The oxidation potentials at low CH4 concentrations (10 ppm of volume) were relatively high in all the secondary forest sites of both ADE and adjacent soils. CH4 oxidation by the ADE soil only recently converted to a manioc plantation was also relatively high. In contrast, both the adjacent soils used for manioc cultivation and the ADE soil with a long history of agriculture displayed lower CH4 uptake rates. Amplicon pyrosequencing of pmoA genes indicated that USCα, Methylocystis and the tropical upland soil cluster (TUSC) were the dominant groups depending on the site. By qPCR analysis it was found that USCα pmoA genes, which are believed to belong to atmospheric CH4 oxidizers, were more abundant in ADE than adjacent soil. USCα pmoA genes were abundant in both forested and cultivated ADE soil, but were below the qPCR detection limit in manioc plantations of adjacent soil. The results indicate that ADE soils can harbor high abundances of atmospheric CH4 oxidizers and are potential CH4 sinks, but as in other upland soils this activity can be inhibited by the conversion of forest to agricultural plantations.

Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

“…The clusters are consistently found in forest soils, often as most abundant group, they are quite frequently detected in grassland soils, but rarely detected in intensively managed agricultural soils (Knief et al, 2006 ; Dunfield, 2007 ). It has been reported that populations decrease and become inactive when forest soils are converted into agricultural soils, or grasslands are subjected to grazing (Knief et al, 2005 ; Abell et al, 2009 ; Dörr et al, 2010 ; Lima et al, 2014 ). They recover in afforested or reforested sites and grassland soil in which nitrogen fertilization is reduced (Nazaries et al, 2011 ; Shrestha et al, 2012 ).…”

“…It shows similarities in dispersal to USCγ, as it is largely absent in wetlands and acidic soils (Kolb, 2009 ; Martineau et al, 2014 ). Moreover, it shows reduced occurrence in intensively managed agricultural soils (Lima et al, 2014 ) with the exception that it has been found in some agricultural fields that are subjected to organic farming and/or that are characterized by higher carbon content (upon biochar or organic residue application; Dörr et al, 2010 ; Lima et al, 2014 ; Ho et al, 2015 ).…”

The microbiomes and metagenomes of forest biochars

“…Instead, most previous work has only used high-throughput sequencing to compare soil with biochars to soil without biochars (e.g. 3 22 23 24 25 ). Consequently, much remains to be learned about the biotic communities of biochars and their metabolic potential in other soil systems.…”

Compositional and functional stability of aerobic methane consuming communities in drained and rewetted peat meadows

“…The primers A189f-Forest675r targeting specifically USC-α pmoA genes were used (Kolb et al 2003). We followed the protocol as described in Lima, Muniz and Dumont (2014). These assays were performed with the CFX96 qPCR cycler (Bio-Rad, München, Germany).…”