Characterization of methanogenic and methanotrophic assemblages in landfill samples

Abstract

A greater understanding of the tightly linked trophic groups of anaerobic and aerobic bacteria residing in municipal solid waste landfills will increase our ability to control methane emissions and pollutant fate in these environments. To this end, we characterized the composition of methanogenic and methanotrophic bacteria in samples taken from two regions of a municipal solid waste landfill that varied in age. A method combining polymerase chain reaction amplification, restriction fragment length polymorphism analysis and phylogenetic analysis was used for this purpose. 16S rDNA sequence analysis revealed a rich assemblage of methanogens in both samples, including acetoclasts, H2/CO2-users and formate-users in the newer samples and H2/CO2-users and formate-users in the older samples, with closely related genera including Methanoculleus, Methanofollis, Methanosaeta and Methanosarcina. Fewer phylotypes of type 1 methanotrophs were observed relative to type 2 methanotrophs. Most type 1 sequences clustered within a clade related to Methylobacter, whereas type 2 sequences were broadly distributed among clades associated with Methylocystis and Methylosinus species. This genetic characterization tool promises rapid screening of landfill samples for genotypes and, therefore, degradation potentials.

Effect of earthworms on the community structure of active methanotrophic bacteria in a landfill cover soil

“…Methanotroph diversity in the landfill soil On the basis of pmoA clone libraries and particularly on pmoA microarray results, a high diversity of pmoA sequences related to both types I and II methanotrophs has been retrieved as reported for other landfill biocover soils (Wise et al, 1999;Bodrossy et al, 2003;Uz et al, 2003;Crossman et al, 2004;Stralis-Pavese et al, 2004). In the Ufton landfill biocover soil, types I and II methanotrophs seemed to be highly diverse with several genera being detected, in particular, after pmoA microarray analysis.…”

“…Methanotrophs are currently classified as type I methanotrophs (comprising nine genera among the g-proteobacteria) and type II methanotrophs (comprising four genera among the a-proteobacteria), according to their intracytoplasmic membrane structure, carbon assimilation pathways, fatty acid composition and phylogeny (Hanson and Hanson, 1996). Types I and II methanotrophs cohabit landfill soils (Wise et al, 1999;Bodrossy et al, 2003;Uz et al, 2003;Crossman et al, 2004;Stralis-Pavese et al, 2004). All methanotrophs possess methane monooxygenase (MMO) that catalyses the first step of methane oxidation.…”

Syntrophic-Methanogenic Associations along a Nutrient Gradient in the Florida Everglades

“…Archaeal 16S rRNA genes were amplified with the universal primer 1492R and Archaea-specific primer 23F (5Ј-TGCAGAYCTGGTYGATYCTGCC-3Ј) (3). PCR amplification was performed in a GeneAmp PCR system 2400 (PerkinElmer Applied Biosystems, Norwalk, Conn.) with HotStarTaq Master Mix (Qiagen, Valencia, Calif.) as reported earlier (25).…”

Phylogeny of Acetate-Utilizing Microorganisms in Soils along a Nutrient Gradient in the Florida Everglades

“…E. coli DNA was not detected in the [ 13 C]DNA fractions but was detected in all [ 12 C]DNA fractions (data not shown). Clone libraries were constructed from dense DNA bands and grouped into operational taxonomic units (OTUs) by restriction fragment length polymorphism classification, as described in previous reports (7,8,34). Two or three representatives of each OTU were sequenced and subjected to chimera evaluation (10); two putative chimeric sequences were eliminated from further analysis.…”